Contacts of the strand formed by residues 120 - 129 (chain B) in PDB entry 6H25
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 GLN 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B GLY 3.1 16.5 - - - +
55B PRO* 3.5 1.4 - - - +
56B HIS* 3.3 51.8 + - + +
58B ILE* 4.0 32.9 - - + +
59B ARG* 4.5 2.3 + - - +
64B ARG* 6.1 0.8 - - - +
71B LEU* 3.5 21.1 - - + +
73B ASN* 4.0 25.2 - - + +
118B ARG 4.3 0.4 + - - -
119B SER* 1.3 71.9 - - - +
121B ILE* 1.3 67.9 + - - +
122B ASP* 5.0 4.6 - - - +
124B TYR* 5.7 1.4 + - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 4.3 6.5 - - + -
54B GLY 4.1 3.4 - - - -
55B PRO* 4.0 22.0 - - + -
70B ALA* 4.7 17.3 - - + -
71B LEU 2.9 11.6 + - - +
72B VAL* 3.4 12.4 - - + +
73B ASN* 2.9 24.6 + - - +
111B ILE* 4.9 15.5 - - + -
112B LEU 6.1 0.7 - - - +
113B THR* 6.3 0.2 - - - -
116B HIS* 5.2 7.0 - - + +
119B SER* 5.3 0.4 - - - -
120B GLN* 1.3 79.2 - - - +
122B ASP* 1.3 69.9 + - - +
123B ILE* 4.5 12.3 - - + -
146B VAL* 5.8 0.7 - - + -
151B ILE* 3.7 45.8 - - + -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 3.3 23.7 - - - +
53B TYR* 3.1 38.9 + - - +
54B GLY 3.6 6.6 + - - +
56B HIS* 3.9 18.4 - - + -
73B ASN* 3.3 13.7 - - + +
120B GLN* 4.1 6.0 - - - +
121B ILE* 1.3 72.1 - - - +
123B ILE* 1.3 61.7 + - - +
124B TYR* 3.2 34.8 - - + +
91E PRO* 4.0 6.8 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 5.7 1.1 - - + -
51B VAL 3.9 4.3 - - - +
52B VAL* 4.6 5.4 - - + -
72B VAL* 4.4 7.0 - - + -
73B ASN 2.8 9.3 + - - +
74B CYS* 3.4 22.7 - - + +
75B GLN 3.3 23.4 + - - +
103B LEU* 5.4 3.1 - - + -
107B PHE* 3.8 40.4 - - + -
111B ILE* 5.5 2.5 - - + -
121B ILE* 4.5 10.8 - - + -
122B ASP* 1.3 77.2 - - - +
124B TYR* 1.3 62.6 + - - +
125B VAL* 4.1 11.1 + - + +
142B ALA* 3.8 27.1 - - + +
145B ALA* 6.1 1.1 - - + -
146B VAL* 4.2 17.9 - - + -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU 4.1 0.2 - - - +
50B ALA* 3.4 2.8 - - - +
51B VAL* 2.9 49.1 + - + +
53B TYR* 4.0 15.9 - + - -
73B ASN* 5.0 12.8 + - - -
74B CYS 6.0 0.2 - - - -
75B GLN* 3.3 37.2 - - + +
120B GLN* 5.7 1.0 + - - -
122B ASP* 3.2 39.5 + - + +
123B ILE* 1.3 75.9 - - - +
125B VAL* 1.3 60.0 + - - +
126B GLN 4.3 0.2 - - - -
87E ALA* 3.6 42.6 - - + +
88E SER* 4.8 6.7 - - - +
91E PRO* 4.0 13.0 - - + +
94E GLU* 3.7 18.5 - - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 5.3 0.9 - - + -
49B LEU 3.5 11.0 - - - +
50B ALA* 4.3 6.5 - - + -
75B GLN 3.5 12.0 + - - +
76B TYR* 4.0 9.4 - - + -
77B SER* 3.4 25.3 + - - +
103B LEU* 5.1 9.9 - - + -
123B ILE* 4.2 18.6 - - + +
124B TYR* 1.3 79.0 - - - +
126B GLN* 1.3 66.6 + - - +
127B VAL* 4.8 0.4 - - + -
138B CYS* 3.7 50.7 - - + +
141B ALA* 5.3 1.3 - - + -
142B ALA* 4.3 7.6 - - + -
88E SER* 5.6 0.4 - - - -
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 3.9 0.2 - - - -
49B LEU* 2.8 44.7 + - + +
77B SER* 3.4 19.0 + - - +
78B SER 5.9 0.2 - - - -
79B ALA* 4.9 3.2 - - - +
124B TYR 4.3 0.2 - - - -
125B VAL* 1.3 74.1 - - - +
127B VAL* 1.3 68.0 + - - +
128B LEU* 3.9 10.3 - - + +
84E ASP* 5.5 0.6 + - - -
86E SER* 3.5 14.7 + - - -
88E SER* 2.8 28.5 + - - +
140E LEU* 2.1 59.3 - - + +
142E LEU* 4.5 8.9 - - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 5.3 3.4 - - + -
47B LYS 3.7 15.5 - - - +
48B ALA* 4.8 4.3 - - + -
76B TYR* 4.1 11.7 - - + +
77B SER 3.4 5.5 + - - -
78B SER* 4.4 12.1 + - - +
79B ALA* 3.1 27.4 + - - +
82B SER* 4.9 1.5 - - - +
125B VAL* 4.8 0.9 - - + -
126B GLN* 1.3 76.6 - - - +
128B LEU* 1.3 63.1 + - - +
129B GLN 3.8 9.9 - - - +
130B ALA* 4.2 22.7 - - + +
134B THR* 4.0 14.1 - - + -
137B ALA* 6.2 0.4 - - + -
138B CYS* 3.4 33.4 - - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 5.4 2.2 - - + -
47B LYS* 3.3 25.2 + - + +
48B ALA 5.2 0.7 - - - -
49B LEU* 3.9 25.8 - - + +
79B ALA* 4.5 8.0 - - - +
81B PHE* 4.0 22.9 - - + +
82B SER* 4.6 5.6 - - - -
126B GLN* 3.9 27.4 - - + +
127B VAL* 1.3 76.9 - - - +
129B GLN* 1.3 61.4 + - + +
41E VAL* 5.8 2.5 - - + -
42E VAL* 4.2 13.4 - - + +
59E LEU* 4.0 31.0 - - + -
140E LEU* 5.2 8.7 - - + -
142E LEU* 5.3 4.9 - - + -
289E PHE* 5.0 17.5 - - + -
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN* 3.3 25.1 + - + +
46B THR* 3.0 9.5 - - - +
47B LYS* 2.9 51.7 + - + +
82B SER* 4.5 4.9 - - - -
127B VAL* 3.7 3.4 - - - +
128B LEU* 1.3 81.7 - - + +
130B ALA* 1.3 63.0 + - - +
131B ASP* 5.8 0.7 - - + -
42E VAL* 4.0 6.7 - - + +
43E SER* 3.3 47.7 + - - +
44E ASN* 3.4 27.7 + - + +
20J VAL* 5.4 3.2 + - - +
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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