Contacts of the strand formed by residues 104 - 117 (chain H) in PDB entry 1S9C
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 104 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ALA* 3.2 1.9 - - - -
22H TYR* 2.9 45.8 + - - -
101H PRO* 5.0 2.9 - - - -
103H ALA* 1.3 78.4 - - - +
105H LYS* 1.3 66.3 + - - -
106H LEU* 5.0 0.9 - - - -
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Residues in contact with LYS 105 (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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19H SER* 6.4 0.7 - - - -
20H TYR 3.3 3.6 - - - +
21H ALA* 3.4 24.7 - - + -
104H GLY* 1.3 73.9 - - - -
106H LEU* 1.3 75.0 + - - +
131H TYR 4.5 0.9 - - - +
132H SER* 4.2 9.2 + - - -
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Residues in contact with LEU 106 (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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19H SER* 3.0 7.8 - - - -
20H TYR* 2.5 42.0 + - + +
22H TYR* 4.0 15.3 - - + +
64H ILE* 3.4 45.8 - - + -
100H LEU* 5.3 3.6 - - + -
101H PRO* 5.6 7.4 - - + -
104H GLY 5.0 0.4 - - - -
105H LYS* 1.3 86.6 - - - +
107H LYS* 1.3 60.4 + - - +
108H CYS* 4.6 1.6 - - - -
130H SER* 4.5 12.1 - - - -
131H TYR 3.4 20.0 - - - +
132H SER* 3.9 4.5 - - - +
137H ILE* 3.7 28.7 - - + -
138H CYS* 5.8 0.2 - - - -
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Residues in contact with LYS 107 (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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17H PRO* 4.5 13.7 - - + -
18H PHE 3.7 8.1 - - - +
19H SER* 4.1 4.9 - - - +
106H LEU* 1.3 73.9 - - - +
108H CYS* 1.3 63.5 + - - +
109H GLU* 3.3 31.1 + - - +
129H TYR 3.6 1.4 - - - +
130H SER* 3.3 3.3 - - - -
131H TYR* 3.1 43.1 + - + +
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Residues in contact with CYS 108 (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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17H PRO* 3.4 5.2 - - - +
18H PHE* 2.5 76.9 + - + +
20H TYR* 4.4 4.7 - - - -
64H ILE* 3.7 20.0 - - - -
65H GLY* 4.8 0.2 - - - -
106H LEU 4.3 8.5 - - - -
107H LYS* 1.3 77.2 - - - +
109H GLU* 1.3 65.6 - - - +
110H ALA 4.1 0.4 - - - -
128H VAL* 4.0 7.9 - - + -
129H TYR 3.3 2.9 - - - +
130H SER* 3.5 20.4 - - - -
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LYS* 5.2 18.3 + - - -
15H LEU 5.6 0.4 - - - -
17H PRO* 4.3 16.8 - - + -
107H LYS* 3.3 30.3 + - + +
108H CYS* 1.3 79.8 - - - +
110H ALA* 1.3 63.2 + - - +
111H VAL* 4.3 6.3 - - + +
127H ASP 3.7 0.9 - - - +
128H VAL* 3.1 4.9 - - - -
129H TYR* 3.0 40.2 + - + +
131H TYR* 3.9 26.9 + - + -
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Residues in contact with ALA 110 (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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14H LYS* 4.1 0.5 - - - +
15H LEU* 3.1 49.8 + - + +
16H PRO 5.1 2.3 + - - +
18H PHE* 4.3 17.5 - - + -
108H CYS 4.1 1.4 + - - -
109H GLU* 1.3 71.2 - - - +
111H VAL* 1.3 74.6 + - - +
126H MET* 3.8 10.1 - - + -
127H ASP 3.3 6.7 - - - +
128H VAL* 4.0 10.8 - - + -
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Residues in contact with VAL 111 (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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12H GLY 5.7 0.4 - - - -
14H LYS* 3.6 35.7 - - + +
15H LEU* 4.1 4.9 - - - +
109H GLU* 4.3 9.6 - - + +
110H ALA* 1.3 89.5 - - - +
112H VAL* 1.3 64.3 + - - +
113H ALA* 2.6 21.9 + - - +
126H MET* 3.7 5.7 - - - +
127H ASP* 2.9 32.8 + - + +
129H TYR* 5.6 7.2 - - + -
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H GLY* 3.1 28.6 - - - +
13H GLN 3.9 22.1 + - - +
15H LEU* 4.6 15.4 - - + +
111H VAL* 1.3 73.7 - - - +
113H ALA* 1.3 61.1 + - - +
114H ASP 3.7 22.0 - - - +
115H VAL* 3.9 16.8 - - + -
124H ILE* 4.4 12.6 - - + -
125H ILE 3.8 4.9 - - - +
126H MET* 4.3 15.9 - - + +
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Residues in contact with ALA 113 (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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12H GLY* 4.6 3.5 - - - -
111H VAL* 2.6 16.9 + - + +
112H VAL* 1.3 72.3 - - - +
114H ASP* 1.3 60.0 + - - +
125H ILE* 2.9 22.0 + - + +
127H ASP* 3.4 26.5 - - + +
160H LYS* 2.8 41.6 - - + +
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Residues in contact with ASP 114 (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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12H GLY* 4.8 5.6 - - - +
112H VAL* 3.1 7.6 - - - +
113H ALA* 1.3 83.6 - - - +
115H VAL* 1.3 100.9 + - - +
116H LEU* 3.3 10.6 - - - +
124H ILE* 3.3 4.0 - - - -
125H ILE* 2.9 43.3 + - + +
155H LYS* 3.4 28.1 + - - -
158H SER* 3.8 11.3 + - - +
160H LYS* 3.9 11.3 - - + +
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Residues in contact with VAL 115 (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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12H GLY 5.3 6.8 - - - +
112H VAL* 3.9 16.2 - - + -
114H ASP* 1.3 104.9 + - - +
116H LEU* 1.3 67.4 + - - +
117H ASP 4.3 0.4 - - - +
122H VAL* 3.2 25.4 - - + -
123H VAL 3.2 8.1 - - - +
124H ILE* 4.1 12.8 - - + +
125H ILE* 6.2 0.2 - - - -
155H LYS* 5.6 0.2 - - - -
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Residues in contact with LEU 116 (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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114H ASP* 3.3 12.3 - - - +
115H VAL* 1.3 84.7 - - - +
117H ASP* 1.3 65.9 + - - +
118H LYS* 3.2 14.3 + - - +
122H VAL* 3.0 5.6 - - - +
123H VAL* 2.6 51.1 + - + -
125H ILE* 5.5 2.2 - - + -
154H GLY* 5.9 0.2 - - - -
155H LYS* 3.2 44.9 - - + +
156H ARG 3.1 26.7 - - - +
157H THR* 4.0 11.9 - - - +
158H SER* 4.3 8.3 - - - +
161H VAL* 5.9 0.9 - - + -
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Residues in contact with ASP 117 (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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115H VAL* 5.2 0.2 - - - +
116H LEU* 1.3 72.8 - - - +
118H LYS* 1.3 87.3 + - - +
119H GLY* 3.0 21.3 + - - +
121H GLY 4.3 1.2 - - - +
122H VAL* 3.9 9.1 - - - +
154H GLY* 4.3 25.7 + - - +
155H LYS 4.6 4.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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