Contacts of the strand formed by residues 74 - 79 (chain A) in PDB entry 2YGE
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LYS* 2.7 52.9 + - + -
72A GLN* 3.5 21.1 - - + +
73A LYS* 1.3 76.7 - - - +
75A LEU* 1.3 61.0 + - - +
76A GLU* 3.9 16.6 - - + +
174A ARG* 3.7 23.8 - - + -
175A LEU 3.2 8.5 - - - +
176A PHE* 3.5 39.5 - - + -
177A LEU* 4.8 0.2 - - - -
185A LEU* 3.1 9.4 - - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 4.0 28.3 - - + -
31A LEU* 4.9 7.2 - - + -
66A ILE* 3.8 24.5 - - + -
67A THR 3.9 0.7 - - - -
68A PRO* 3.8 21.3 - - + -
73A LYS 4.4 0.2 + - - -
74A VAL* 1.3 73.9 - - - +
76A GLU* 1.3 62.9 + - - +
77A ILE* 4.1 19.1 - - + -
173A LEU 3.5 1.7 - - - +
175A LEU* 2.8 37.8 + - + +
177A LEU* 4.3 20.1 - - + +
184A TYR* 3.6 27.6 - - + +
185A LEU* 4.5 0.4 - - + -
190A ILE* 4.0 6.1 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG 3.7 0.6 - - - +
66A ILE* 3.3 8.0 - - - +
67A THR* 3.0 47.0 + - - +
69A LYS* 2.7 39.2 + - - +
74A VAL* 3.9 11.9 - - + -
75A LEU* 1.3 77.0 - - - +
77A ILE* 1.3 64.8 + - - +
78A ARG* 4.1 2.5 - - + -
165A GLU* 4.5 5.9 - - - +
172A ILE* 3.9 31.0 - - + +
173A LEU 3.2 3.4 - - - +
174A ARG* 2.8 33.2 + - + +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.1 19.7 - - + -
34A LEU* 4.0 44.4 - - + +
35A ILE* 5.0 3.6 - - + +
38A ALA* 5.0 3.1 - - + -
64A ILE* 4.6 18.8 - - + -
65A ARG 3.7 2.7 - - - -
66A ILE* 4.5 10.5 - - + +
75A LEU* 4.1 24.5 - - + +
76A GLU* 1.3 79.5 - - - +
78A ARG* 1.3 61.7 + - - +
79A ASP* 5.2 0.9 - - - +
171A THR 3.7 1.4 - - - +
172A ILE* 3.6 1.4 - - - -
173A LEU* 2.8 52.6 + - + +
175A LEU* 4.1 10.3 - - + -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 5.3 0.2 - - - -
59A GLU* 4.4 12.5 + - - +
63A PHE* 4.1 28.0 - - + -
64A ILE* 3.3 7.9 - - - +
65A ARG* 2.8 66.6 + - + +
76A GLU* 4.1 2.2 - - + -
77A ILE* 1.3 75.3 - - - +
79A ASP* 1.3 72.6 + - - +
80A SER* 6.0 0.6 - - - +
165A GLU* 3.6 25.6 + - - -
166A ARG 4.5 3.6 + - - -
167A ILE* 4.0 33.5 - - + +
168A GLY 4.7 2.4 - - - +
169A ARG 5.4 3.6 + - - +
171A THR 3.2 12.1 - - - +
172A ILE* 3.8 24.2 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.7 23.1 - - + +
41A ALA* 3.8 6.5 - - - +
42A LEU* 4.1 7.4 - - + -
63A PHE* 3.3 13.0 - - - +
77A ILE 5.2 0.9 - - - +
78A ARG* 1.3 85.4 + - - +
80A SER* 1.3 59.0 + - - +
81A GLY* 2.7 31.0 + - - +
83A GLY 5.1 0.3 + - - -
169A ARG 3.8 1.0 - - - +
170A GLY* 3.4 2.4 - - - -
171A THR* 3.0 41.5 + - - +
173A LEU* 5.6 0.3 - - - +
1215A GDM 2.7 30.7 + - - -
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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