Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 3W1Y
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 LEU 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.5 6.1 - - + -
32B PRO 3.0 16.5 + - - +
33B ILE* 3.3 20.0 - - + +
34B LEU 2.8 26.3 + - - +
98B ILE* 4.1 15.5 - - + -
109B LEU* 4.5 15.0 - - + +
112B ILE* 4.2 18.4 - - + -
113B TYR* 3.9 23.3 - - + +
116B ALA* 3.9 36.8 - - + +
117B LYS* 4.2 3.1 - - - +
121B GLY 3.8 0.8 + - - -
122B PHE* 1.3 70.3 - - - +
124B TYR* 1.3 62.7 + - - +
125B VAL* 3.7 15.2 + - + -
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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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5B TYR* 3.6 52.3 + + + -
7B TYR* 4.0 4.8 - - + -
8B GLN* 3.4 38.5 - - + +
16B ARG* 3.4 10.4 - - - -
34B LEU* 3.5 32.3 - - + -
98B ILE* 4.1 18.7 - - - +
99B GLY 4.6 1.7 + - - -
116B ALA 5.4 1.6 + - - -
118B ASP* 3.6 16.8 - - + +
120B ASP* 2.5 34.2 + - - -
122B PHE* 3.5 21.1 + - + -
123B LEU* 1.3 73.9 - - - +
125B VAL* 1.3 63.3 + - - +
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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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5B TYR* 3.7 5.8 - - - -
33B ILE* 3.6 23.8 - - + -
34B LEU 2.8 12.9 + - - +
35B CYS* 3.3 11.0 - - - -
36B GLU 3.0 23.6 + - - -
78B PHE* 3.8 25.4 - - + -
96B VAL* 3.9 19.1 - - + -
97B PHE 3.4 9.9 - - - +
98B ILE* 3.9 17.9 - - + -
109B LEU* 6.1 0.9 - - + -
123B LEU* 4.1 13.7 - - + +
124B TYR* 1.3 79.9 - - - +
126B SER* 1.3 65.2 + - - +
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Residues in contact with SER 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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5B TYR* 3.5 20.5 + - - -
36B GLU* 3.0 11.0 - - - -
37B PRO 4.6 1.1 - - - -
38B THR* 3.4 23.6 + - - +
96B VAL* 3.3 4.2 - - - +
97B PHE* 2.8 51.6 + - - +
99B GLY 5.0 1.4 + - - -
125B VAL* 1.3 75.7 - - - +
127B TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 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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35B CYS* 3.6 22.0 - - + -
36B GLU* 2.9 20.3 + - - -
37B PRO* 3.3 40.3 - - + +
38B THR* 2.9 27.8 + - - -
63B ASP* 4.6 6.5 + - - +
65B ASN* 5.9 1.1 + - + -
82B LEU* 3.9 26.5 - - + -
86B LEU* 4.0 35.7 - - + +
94B VAL* 4.2 3.1 - - + -
95B PHE* 3.3 11.2 - - - +
96B VAL* 4.1 3.4 - - + -
126B SER* 1.3 75.9 - - - +
128B GLY* 1.3 67.6 + - - +
129B VAL* 5.1 6.7 - - + -
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Residues in contact with GLY 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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38B THR* 4.9 1.6 - - - -
94B VAL* 3.3 6.8 - - - +
95B PHE* 2.9 54.9 + - - -
127B TYR* 1.3 82.1 - - - +
129B VAL* 1.3 63.5 + - - -
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Residues in contact with VAL 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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86B LEU* 5.1 9.6 - - + -
88B LEU* 3.8 35.7 - - + -
92B GLN* 3.8 29.8 - - + +
93B ALA 3.3 10.1 - - - +
94B VAL* 5.5 1.6 - - + -
95B PHE* 3.5 7.2 - - - -
127B TYR* 5.1 7.0 - - + -
128B GLY* 1.3 78.2 - - - +
130B GLU* 1.3 64.1 + - - +
131B ASN* 5.3 0.7 - - - +
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Residues in contact with GLU 130 (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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92B GLN* 3.2 4.9 - - - +
93B ALA* 2.8 46.6 + - + +
94B VAL 4.5 4.5 - - - +
95B PHE* 3.8 32.1 - - + +
129B VAL* 1.3 75.4 - - - +
131B ASN* 1.3 73.0 + - - +
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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