Contacts of the helix formed by residues 116 - 138 (chain H) in PDB entry 6CP3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 116 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H SER* 1.3 80.6 - - - +
117H ALA* 1.3 60.9 + - - +
118H ARG 3.5 1.8 - - - +
119H GLU* 3.3 14.3 + - + +
120H ALA 2.9 24.1 + - - -
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H SER 4.7 0.2 - - - -
116H ASP* 1.3 75.6 - - - +
118H ARG* 1.3 62.9 + - + +
120H ALA* 3.3 5.4 + - - +
121H ALA* 2.9 32.2 + - - +
6I ALA* 5.7 8.5 - - + +
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Residues in contact with ARG 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G ASP* 4.0 18.2 + - - -
152G SER* 4.7 7.1 + - - -
116H ASP* 3.5 0.6 - - - +
117H ALA* 1.3 81.5 - - + +
119H GLU* 1.3 64.0 + - + +
121H ALA* 3.7 3.9 + - - +
122H GLU* 3.5 37.2 + - - +
6I ALA 3.8 8.2 + - - -
7I GLY* 2.6 41.5 + - - -
8I ILE* 4.3 9.3 - - - +
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Residues in contact with GLU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H VAL* 3.8 20.0 - - + +
115H SER* 3.5 21.3 + - - -
116H ASP* 3.3 13.3 + - + +
118H ARG* 1.3 79.6 - - + +
120H ALA* 1.3 60.1 + - - +
122H GLU* 3.4 8.8 + - - +
123H ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H VAL 3.5 14.8 - - - +
113H SER* 3.3 28.9 - - - +
115H SER 3.8 8.1 - - - +
116H ASP 2.9 18.6 + - - +
117H ALA* 3.3 6.0 + - - +
119H GLU* 1.3 73.9 - - - +
121H ALA* 1.3 60.3 + - - +
123H ALA* 3.4 1.7 + - - +
124H ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ALA 2.9 17.2 + - - +
118H ARG 4.1 4.3 - - - +
119H GLU 3.3 0.2 - - - -
120H ALA* 1.3 76.6 - - - +
122H GLU* 1.3 58.0 + - + +
124H ALA* 3.2 7.3 + - - +
125H ILE* 2.9 35.5 + - + +
3I TRP* 5.2 5.5 - - + +
6I ALA* 4.9 5.6 - - + -
7I GLY* 3.7 31.2 - - - +
8I ILE 5.0 0.9 - - - +
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Residues in contact with GLU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ARG* 3.5 25.3 + - - +
119H GLU* 3.4 9.6 + - - +
121H ALA* 1.3 75.0 - - + +
123H ALA* 1.3 61.2 + - - +
125H ILE* 3.3 14.1 + - + +
126H GLN* 3.0 36.2 + - - +
8I ILE* 5.1 10.8 - - + +
12I ALA* 6.1 0.5 - - - +
16I VAL* 3.8 31.8 - - + +
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Residues in contact with ALA 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H LYS* 3.3 28.1 - - + +
112H VAL* 3.7 10.8 - - + -
113H SER* 3.6 15.0 - - - +
119H GLU 2.9 17.0 + - - +
120H ALA 3.4 6.7 - - - +
121H ALA 3.2 0.2 - - - -
122H GLU* 1.3 77.2 - - - +
124H ALA* 1.3 57.5 + - - +
126H GLN* 3.2 10.9 + - - +
127H VAL* 2.9 32.2 + - - +
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Residues in contact with ALA 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H SER* 4.6 7.8 - - - -
120H ALA 2.9 17.4 + - - +
121H ALA* 3.2 7.2 + - - +
123H ALA* 1.3 73.0 - - - +
125H ILE* 1.3 60.8 - - + +
127H VAL* 3.2 10.8 + - - +
128H GLU* 2.9 36.3 + - + +
1I SER 4.8 16.4 - - - +
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Residues in contact with ILE 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H ALA* 2.9 22.8 + - + +
122H GLU* 3.5 15.7 - - + +
123H ALA 3.3 0.2 - - - -
124H ALA* 1.3 77.3 - - + +
126H GLN* 1.3 56.9 + - - +
128H GLU* 3.1 11.7 + - - +
129H VAL* 2.9 37.5 + - + +
1I SER 6.3 0.4 - - - +
3I TRP* 3.9 22.7 - - + -
8I ILE* 4.8 14.6 - - + -
13I TYR* 3.6 53.2 - - + +
16I VAL* 4.0 17.9 - - + -
17I ALA* 4.9 1.3 - - + +
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Residues in contact with GLN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H LYS* 2.8 45.5 + - + +
122H GLU* 3.0 23.0 + - - +
123H ALA* 3.2 6.2 + - - +
125H ILE* 1.3 72.6 - - - +
127H VAL* 1.3 60.6 + - - +
129H VAL* 3.9 6.2 - - - +
130H LEU* 2.9 38.8 + - + +
16I VAL* 3.5 31.8 + - + +
19I GLN* 4.6 11.5 + - - +
20I ALA* 3.7 25.0 - - + +
23I SER* 6.1 0.2 - - - -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ALA* 4.7 2.7 - - + +
109H LYS* 4.4 4.7 - - + -
110H LYS* 3.7 42.0 - - + +
113H SER* 5.3 2.5 - - - -
123H ALA 2.9 21.0 + - - +
124H ALA* 3.4 12.3 - - - +
126H GLN* 1.3 77.3 - - - +
128H GLU* 1.3 59.6 + - + +
130H LEU* 3.4 6.1 + - - +
131H GLU* 2.9 54.8 + - + +
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H ALA* 2.9 23.8 + - - +
125H ILE* 3.5 12.2 - - - +
127H VAL* 1.3 78.6 - - + +
129H VAL* 1.3 54.7 + - + +
131H GLU* 3.4 9.1 + - - +
132H ASN* 2.7 43.6 + - - +
1I SER* 3.7 30.6 + - - -
3I TRP* 4.9 6.4 + - - -
13I TYR* 4.1 18.2 + - - +
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Residues in contact with VAL 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PRO* 4.7 15.3 - - + -
69H PHE* 4.4 19.7 - - + -
71H SER* 6.4 0.4 - - - -
125H ILE* 2.9 29.5 + - + +
126H GLN* 3.9 7.4 - - - +
128H GLU* 1.3 78.2 - - + +
130H LEU* 1.3 58.1 + - + +
132H ASN* 3.2 11.7 + - - +
133H LEU* 2.8 34.4 + - + +
13I TYR* 5.7 3.8 - - + +
17I ALA* 4.4 27.6 - - + +
20I ALA* 4.3 18.4 - - + -
21I ILE* 5.2 1.8 - - - +
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Residues in contact with LEU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LYS* 3.9 31.7 - - + +
105H LEU* 5.1 3.4 - - + -
106H ALA* 3.7 36.6 - - + +
109H LYS* 5.3 8.5 - - + +
126H GLN* 2.9 28.1 + - + +
127H VAL* 3.9 5.4 - - - +
129H VAL* 1.3 77.5 - - + +
131H GLU* 1.3 60.4 + - + +
133H LEU* 3.1 25.9 + - + +
134H GLN* 2.9 29.2 + - - +
20I ALA* 5.3 7.0 - - + +
24I SER* 4.3 10.8 - - - -
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Residues in contact with GLU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LYS* 5.5 4.3 - - - +
127H VAL* 2.9 41.1 + - + +
128H GLU* 3.9 8.0 - - - +
130H LEU* 1.3 75.4 - - + +
132H ASN* 1.3 62.3 + - - +
134H GLN* 3.3 46.5 + - - +
135H SER* 4.1 2.4 + - - -
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Residues in contact with ASN 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PRO* 3.9 26.8 + - - +
55H GLY* 5.6 1.1 - - - -
69H PHE* 4.7 9.0 - - + -
128H GLU* 2.7 32.8 + - - +
129H VAL* 3.2 13.9 + - - +
131H GLU* 1.3 76.1 - - - +
133H LEU* 1.3 58.0 + - - +
134H GLN 3.1 0.4 - - - -
135H SER* 2.4 36.4 + - - +
136H VAL* 3.8 2.1 + - - +
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H PHE* 3.6 40.8 - - + -
91H PHE* 6.0 1.8 - - + -
97H SER* 4.8 8.1 - - - -
102H LYS* 3.3 28.8 + - - +
129H VAL* 2.8 23.9 + - + +
130H LEU* 3.1 36.3 + - + +
132H ASN* 1.3 72.5 - - - +
134H GLN* 1.3 58.7 + - - +
135H SER 3.1 0.2 - - - -
136H VAL* 2.9 17.3 + - + +
137H LEU* 2.9 27.9 + - - +
20I ALA 5.3 2.7 - - - +
21I ILE* 5.5 3.8 - - - -
24I SER* 4.5 9.9 - - - -
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Residues in contact with GLN 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ASN* 5.5 4.6 + - - -
130H LEU* 2.9 16.3 + - - +
131H GLU* 3.3 43.5 + - - +
132H ASN 3.1 0.2 - - - -
133H LEU* 1.3 76.8 - - - +
135H SER* 1.3 55.4 + - - +
137H LEU* 3.2 23.3 + - + +
138H LYS* 2.9 22.0 + - - -
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Residues in contact with SER 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 5.3 5.9 - - - +
67H LYS* 5.9 1.7 - - - -
69H PHE* 5.8 0.2 - - - -
131H GLU 4.1 1.9 + - - -
132H ASN* 2.4 27.0 + - - -
134H GLN* 1.3 77.6 - - - +
136H VAL* 1.3 65.9 + - - +
138H LYS* 3.3 22.1 - - - +
42M SER* 5.4 13.2 - - - -
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Residues in contact with VAL 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H VAL* 4.1 15.0 - - + -
67H LYS* 5.7 9.4 - - - +
69H PHE* 3.6 31.4 - - + -
91H PHE* 4.0 32.8 - - + -
93H LEU 5.4 1.3 - - - +
94H GLU* 4.9 15.6 - - + +
97H SER* 4.6 7.2 - - - +
102H LYS* 4.9 1.1 - - - +
132H ASN 4.1 0.2 - - - +
133H LEU* 2.9 22.1 + - + +
135H SER* 1.3 81.3 - - - +
137H LEU* 1.3 67.7 + - - +
138H LYS* 3.5 6.8 + - - +
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H SER* 4.9 7.6 - - - +
98H GLN* 5.7 0.2 - - - -
99H GLU* 3.4 47.8 - - + +
102H LYS* 3.3 31.0 - - + +
103H ASN* 6.1 2.0 - - - +
133H LEU 2.9 13.0 + - - +
134H GLN* 3.2 31.2 + - + +
136H VAL* 1.3 74.4 - - - +
138H LYS* 1.3 70.8 + - - +
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Residues in contact with LYS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H LYS* 5.9 5.7 - - - +
94H GLU* 5.8 4.5 - - - +
134H GLN 2.9 12.9 + - - -
135H SER* 3.3 21.1 - - - +
136H VAL 3.2 8.3 - - - +
137H LEU* 1.3 83.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il