Contacts of the helix formed by residues 114 - 130 (chain H) in PDB entry 4D1Q
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 GLY 114 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G ASP* 3.1 24.9 - - - -
107G ARG* 4.9 2.7 - - - -
110H SER 3.2 11.3 + - - -
111H ALA 3.4 3.0 + - - -
112H VAL 3.4 2.0 - - - -
113H SER* 1.3 78.1 + - - +
115H SER* 1.3 62.9 + - - -
117H PHE* 3.3 6.1 + - - +
118H ILE* 3.1 18.4 + - - +
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Residues in contact with SER 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ARG* 3.1 23.3 - - - -
105G ASP* 3.3 4.3 + - - -
113H SER 3.3 4.9 + - - -
114H GLY* 1.3 67.4 - - - -
116H GLY* 1.3 66.1 + - - +
117H PHE 3.0 3.3 + - - -
118H ILE* 3.2 10.5 + - - +
119H ASP* 3.1 29.1 + - - +
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Residues in contact with GLY 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LYS 4.4 0.9 - - - +
100G GLN* 5.6 0.7 - - - +
101G TRP* 3.4 23.1 + - - +
104G ARG* 3.7 33.7 - - - +
105G ASP* 2.8 19.7 + - - -
115H SER* 1.3 74.3 - - - +
117H PHE* 1.3 55.8 + - - +
119H ASP* 3.8 2.9 + - - +
120H MET* 3.2 18.9 + - - +
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Residues in contact with PHE 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TRP* 3.1 39.3 - + + +
105G ASP* 3.3 4.9 + - - +
117G PHE* 4.9 2.2 - + - -
120G MET* 4.0 20.4 - - + -
124G PHE* 4.8 0.2 - + - -
141G LEU* 3.8 14.1 - - + -
101H TRP* 3.6 31.9 - + - -
111H ALA 3.7 7.0 - - - +
112H VAL* 3.1 35.7 - - + -
114H GLY 3.3 8.9 + - - +
116H GLY* 1.3 73.7 - - - +
118H ILE* 1.3 57.2 + - - +
119H ASP 3.0 1.3 - - - -
120H MET* 2.8 17.4 + - + +
121H ILE* 2.7 65.7 + - + +
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G VAL* 4.0 12.9 - - + +
138G GLU* 3.4 32.8 - - + +
141G LEU* 4.5 10.5 - - + -
112H VAL 4.0 11.2 - - - +
113H SER* 3.4 24.2 - - - +
114H GLY 3.1 12.9 + - - +
115H SER* 3.7 12.3 - - - +
117H PHE* 1.3 79.1 - - - +
119H ASP* 1.3 61.0 + - - +
121H ILE* 3.7 6.5 + - - +
122H LYS* 3.1 39.1 + - - +
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Residues in contact with ASP 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LYS* 3.7 23.6 - - - +
100G GLN* 6.1 0.4 - - - +
104G ARG* 3.5 24.1 + - - +
115H SER* 3.1 17.5 + - - +
116H GLY 3.9 4.7 - - - +
117H PHE 3.0 0.6 - - - -
118H ILE* 1.3 83.8 - - - +
120H MET* 1.3 62.7 + - - +
122H LYS* 3.5 20.9 + - - +
123H PHE 3.4 14.4 + - - -
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Residues in contact with MET 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LYS* 3.7 29.2 - - + +
98G CYS* 3.6 29.6 - - - -
101G TRP* 3.8 28.7 - - + -
117G PHE* 4.3 13.2 - - + -
121G ILE* 4.6 1.3 - - + -
116H GLY 3.2 15.4 + - - +
117H PHE* 2.8 27.6 + - + +
119H ASP* 1.3 74.3 - - - +
121H ILE* 1.3 89.4 + - + +
123H PHE* 3.3 5.1 + - + +
124H PHE* 3.2 32.9 + - + -
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Residues in contact with ILE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ILE* 4.4 11.2 - - + -
124G PHE* 4.0 41.2 - - + +
137G VAL* 4.1 10.8 - - + -
140G LEU* 5.6 0.4 - - + -
141G LEU* 4.1 15.5 - - + -
117H PHE* 2.7 50.6 + - + +
118H ILE 3.9 5.4 - - - +
120H MET* 1.3 101.6 - - + +
122H LYS* 1.3 61.9 + - - +
124H PHE* 3.5 6.3 + - + +
125H ILE* 3.1 24.5 + - + +
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Residues in contact with LYS 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G VAL 5.7 0.6 + - - -
137G VAL* 3.5 30.0 - - + +
138G GLU* 4.1 14.2 + - - -
118H ILE* 3.1 36.5 + - - +
119H ASP* 3.6 21.8 - - - +
120H MET 3.2 0.2 - - - -
121H ILE* 1.3 76.9 - - - +
123H PHE* 1.3 56.0 + - - +
125H ILE* 2.9 10.9 + - - +
126H LYS* 2.8 28.3 + - - +
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Residues in contact with PHE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G CYS* 3.6 11.7 - - - -
93G GLU* 3.3 43.7 - - + -
94G ALA* 3.2 35.0 - - + -
97G LYS* 3.5 32.3 - - + -
119H ASP 3.4 2.8 + - - -
120H MET* 3.3 10.0 + - + +
122H LYS* 1.3 79.9 - - - +
124H PHE* 1.3 93.5 + + - +
126H LYS* 3.3 18.1 - - - +
127H VAL* 3.1 38.2 + - + +
140H LEU* 5.1 0.2 - - + -
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Residues in contact with PHE 124 (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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94G ALA* 4.5 3.4 - - + -
98G CYS* 4.0 17.7 - - - -
117G PHE* 5.2 0.7 - + - -
121G ILE* 3.7 38.6 - - + +
124G PHE* 4.6 12.3 - - + -
125G ILE* 3.8 17.8 - - + +
120H MET* 3.2 33.3 + - + +
121H ILE* 3.5 7.4 + - + +
122H LYS 3.2 0.2 - - - -
123H PHE* 1.3 102.7 - + - +
125H ILE* 1.3 65.5 + - - +
126H LYS 3.0 1.6 - - - -
127H VAL* 3.2 9.9 + - + +
128H GLY 3.1 17.5 + - - -
140H LEU* 3.9 25.1 - - + -
141H LEU* 3.5 25.1 - - + -
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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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124G PHE* 3.9 27.4 - - + +
127G VAL* 4.4 7.6 - - + -
128G GLY* 3.4 14.5 - - - -
132G GLY 4.1 4.2 - - - +
133G GLU* 4.3 9.0 - - + +
135G VAL* 3.6 37.5 - - + -
137G VAL* 4.3 13.2 - - + -
140G LEU* 4.1 26.5 - - + -
121H ILE* 3.1 19.1 + - + +
122H LYS* 2.9 10.8 + - - +
124H PHE* 1.3 76.1 - - - +
126H LYS* 1.3 62.5 + - - +
128H GLY 3.3 0.7 + - - -
129H ALA* 3.3 19.9 + - - +
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Residues in contact with LYS 126 (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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93G GLU* 3.2 27.1 + - - -
133G GLU* 3.2 37.8 - - + +
122H LYS 2.8 12.0 + - - +
123H PHE* 3.3 22.2 - - + +
125H ILE* 1.3 79.1 - - - +
127H VAL* 1.3 62.2 + - + +
128H GLY 3.3 0.3 + - - -
129H ALA* 3.4 2.3 + - - +
130H GLU* 3.2 32.1 + - + +
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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
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86G VAL* 4.1 13.0 - - + -
90G CYS* 3.7 32.5 - - - -
125G ILE* 4.6 5.5 - - + +
123H PHE* 3.1 38.2 + - + +
124H PHE* 3.2 14.1 + - + +
126H LYS* 1.3 76.7 - - + +
128H GLY* 1.3 61.0 + - - +
130H GLU* 3.7 2.5 + - - -
131H TYR* 3.1 45.9 + - + +
135H VAL* 4.9 6.1 - - + -
140H LEU* 4.5 11.2 - - + -
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Residues in contact with GLY 128 (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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125G ILE* 3.2 35.4 - - - +
129G ALA* 3.2 18.6 + - - +
124H PHE 3.1 10.3 + - - -
125H ILE 3.3 4.0 + - - -
126H LYS 3.2 0.4 - - - -
127H VAL* 1.3 75.8 - - - +
129H ALA* 1.3 59.5 + - - +
132H GLY* 3.0 24.6 + - - -
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Residues in contact with ALA 129 (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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128G GLY 3.3 11.0 - - - +
129G ALA* 3.8 4.1 - - - +
132G GLY* 3.3 37.7 - - - +
133G GLU* 4.1 8.5 - - + +
125H ILE 3.3 10.1 + - - +
126H LYS 3.4 3.6 + - - +
128H GLY* 1.3 76.5 - - - +
130H GLU* 1.3 57.0 + - - +
131H TYR 3.2 4.2 + - - -
132H GLY 4.0 3.1 + - - -
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Residues in contact with GLU 130 (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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90G CYS* 5.6 3.8 - - - +
126H LYS* 3.2 24.4 + - + +
127H VAL* 3.7 2.0 - - - -
129H ALA* 1.3 76.4 - - - +
131H TYR* 1.3 96.7 + - + +
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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