Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 6W4E
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 MET 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 3.1 24.7 - - + +
80B CYS* 4.5 10.5 - - - -
97B ARG* 3.9 39.3 - - + +
100B ILE* 4.0 20.9 - - + -
101B LYS* 6.1 2.0 - - + -
107B GLU 5.0 5.8 - - - +
109B VAL* 3.1 29.7 + - + +
110B PRO* 1.3 79.2 - - - +
112B VAL* 1.3 69.6 + - - +
137B TYR* 5.0 6.7 - - + +
139B ILE* 3.2 43.5 - - + +
140B PRO* 3.9 3.3 - - - +
159B LEU* 4.2 0.2 - - - -
162B GLU* 4.3 6.5 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE 3.0 6.9 + - - -
79B LEU* 3.6 18.5 - - + +
80B CYS* 2.8 28.9 + - - +
111B MET* 1.3 80.3 - - - +
113B LEU* 1.3 69.8 + - - +
114B VAL* 3.8 4.8 + - + -
139B ILE* 4.1 5.2 - - - -
140B PRO* 3.6 14.8 - - + +
142B ILE* 4.7 4.5 - - + -
155B ALA* 4.9 1.1 - - - +
158B THR* 3.9 24.5 - - + -
159B LEU* 3.6 35.2 - - + +
162B GLU* 3.6 15.0 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 3.8 23.3 - - + +
82B PHE* 3.6 30.1 - - + -
90B PHE* 5.1 5.4 - - + -
93B ILE* 3.8 16.8 - - + -
112B VAL* 1.3 73.4 - - - +
114B VAL* 1.3 62.8 + - - +
130B ALA* 3.6 25.8 - - + +
133B LEU* 5.7 4.0 - - + -
134B ALA* 3.9 12.8 - - + +
137B TYR* 6.1 2.5 - - + -
139B ILE* 3.7 16.9 - - + +
140B PRO 3.1 13.8 + - - +
141B PHE* 3.4 19.4 - - + -
142B ILE* 3.3 23.2 + - - +
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Residues in contact with VAL 114 (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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19B LEU* 4.0 22.2 - - + -
79B LEU* 3.7 37.5 - - + -
80B CYS 2.8 13.9 + - - +
81B VAL* 3.4 9.6 - - + -
82B PHE* 3.0 29.8 + - - -
112B VAL* 4.4 5.6 - - + -
113B LEU* 1.3 77.2 - - - +
115B GLY* 1.3 60.2 + - - +
116B ASN 3.4 1.6 + - - -
142B ILE* 4.1 3.8 - - + +
144B THR* 3.3 29.2 - - + +
155B ALA* 4.9 14.6 - - + -
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Residues in contact with GLY 115 (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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82B PHE* 3.7 13.2 - - - -
84B ILE* 4.3 3.8 - - - -
114B VAL* 1.3 70.5 - - - +
116B ASN* 1.3 61.4 + - - -
118B CYS* 3.1 11.1 - - - -
141B PHE* 3.4 29.4 - - - -
142B ILE 3.5 5.7 + - - -
143B GLU 3.8 0.2 - - - -
144B THR 2.8 28.5 + - - +
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Residues in contact with ASN 116 (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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14B VAL 2.8 28.2 + - - +
15B GLY* 3.7 9.7 + - - -
19B LEU* 3.6 20.7 - - + +
81B VAL* 4.0 12.3 - - + -
82B PHE 2.9 13.2 + - - +
84B ILE* 3.2 19.8 + - - +
114B VAL* 3.4 1.8 + - + -
115B GLY* 1.3 72.8 - - - +
117B LYS* 1.3 80.4 + - - +
118B CYS 3.2 3.6 + - - -
144B THR* 3.3 7.6 - - - +
146B ALA 3.3 14.4 + - - -
201B GSP 2.9 34.2 + - - +
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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