Contacts of the strand formed by residues 178 - 183 (chain B) in PDB entry 6VWW
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 ASN 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU 3.6 0.2 - - - +
144B ILE* 3.1 9.0 - - - +
145B THR* 2.7 35.1 + - - +
146B GLU 4.4 1.0 + - - -
147B GLY* 2.8 35.2 + - - -
148B SER* 4.0 3.0 - - - +
154B PRO* 3.8 19.1 - - + +
155B SER 3.4 3.1 - - - -
156B VAL* 4.1 11.1 - - - +
177B PHE* 1.3 76.0 - - - +
179B TYR* 1.3 60.3 + - - +
180B TYR* 3.3 24.5 + - + +
407B ACY 2.8 23.9 + - - +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.2 28.7 - - + +
72B ILE* 3.8 24.7 - - + +
73B LEU* 5.2 2.5 - - + -
76B LEU* 3.8 20.2 - - + -
142B VAL* 4.7 3.8 - - + -
143B LEU 3.4 3.6 - - - -
144B ILE* 3.6 23.8 - - + -
153B GLN 4.6 0.9 - - - +
154B PRO 4.1 0.3 - - - -
155B SER* 2.7 36.2 + - - +
157B GLY* 3.5 34.1 - - - -
158B PRO* 4.0 12.0 - - + +
177B PHE* 3.6 22.1 - + + -
178B ASN* 1.3 76.7 - - - +
180B TYR* 1.3 68.1 + - - +
190B LEU* 3.6 19.7 - - + +
325B TYR* 3.9 7.2 - + - +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.8 21.1 - - + -
142B VAL* 3.2 8.1 - - - +
143B LEU* 2.7 55.4 + - + +
145B THR* 3.1 30.5 + - + -
147B GLY 3.6 3.8 + - - -
148B SER* 4.3 0.3 - - - -
149B VAL* 3.8 17.3 + - + -
152B LEU* 3.7 32.2 + - + -
153B GLN 3.8 9.6 - - - -
154B PRO* 3.5 22.9 - - + +
178B ASN* 3.3 35.8 + - + +
179B TYR* 1.3 78.4 - - - +
181B LYS* 1.3 61.1 - - - +
187B VAL* 5.7 5.8 - - + -
188B GLN 5.7 0.2 - - - -
190B LEU* 4.6 4.3 - - - -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN 5.4 0.8 + - - -
76B LEU* 3.5 36.7 + - + +
121B THR* 5.5 5.2 - - + -
135B PHE* 4.1 0.4 - - - -
141B GLY 3.4 11.2 - - - +
142B VAL* 4.0 9.6 - - + -
180B TYR* 1.3 77.2 - - - +
182B LYS* 1.3 66.1 + - - +
183B VAL* 3.7 23.2 - - + +
187B VAL* 3.4 7.4 - - - +
188B GLN* 2.8 45.8 + - + +
190B LEU* 4.0 28.6 - - + +
403B GOL 6.1 0.9 - - - -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 5.2 1.6 + - - +
135B PHE* 3.2 40.5 + - + +
136B ARG* 2.8 29.1 + - - +
137B ASN 4.4 0.2 - - - -
138B ALA 2.5 27.1 + - - +
139B ARG 3.9 7.4 - - - +
140B ASN* 3.4 3.8 - - - +
141B GLY 2.9 35.0 + - - +
181B LYS* 1.3 73.6 - - - +
183B VAL* 1.3 68.9 + - - +
185B GLY* 3.8 25.9 + - - -
186B VAL 3.4 4.9 - - - +
187B VAL* 3.7 26.5 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 5.9 1.8 - - - +
140B ASN* 3.5 9.4 - - + +
181B LYS* 3.7 22.2 - - - +
182B LYS* 1.3 77.3 - - - +
184B ASP* 1.3 87.2 + - - +
185B GLY 3.3 0.2 - - - -
186B VAL* 2.8 25.2 + - - +
188B GLN* 3.6 32.0 - - + +
403B GOL 6.0 0.9 - - - +
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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
------------------------------------------------------------
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