Contacts of the strand formed by residues 74 - 79 (chain A) in PDB entry 4GQG
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 PHE 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 10.1 - - + -
11A ALA* 4.8 8.7 - - + -
12A LYS 3.5 26.2 - - - -
13A MET* 3.5 46.9 - - + -
14A PRO* 3.7 20.6 - - + -
41A ARG 2.8 12.2 + - - +
42A HIS* 3.2 9.2 - + - -
43A ILE 3.1 22.7 + - - -
72A ASP 5.2 0.4 - - - +
73A LEU* 1.4 76.2 - - - +
75A ILE* 1.3 60.2 + - - +
76A VAL* 3.9 9.9 - - + -
106A ASP* 3.3 20.6 - - + -
107A VAL* 3.6 28.7 - - + -
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Residues in contact with ILE 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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41A ARG 4.5 0.2 - - - +
43A ILE* 3.8 27.6 - - + +
45A CYS* 4.3 10.5 - - - -
59A ILE* 3.8 24.7 - - + -
70A ARG* 4.1 17.0 - - - +
73A LEU* 4.2 17.5 - - + -
74A PHE* 1.3 78.8 - - - +
76A VAL* 1.4 63.1 + - - +
100A LEU* 4.1 17.7 - - + -
102A LEU* 3.9 32.3 - - + -
105A LEU* 4.0 5.7 - - + +
106A ASP* 2.8 37.1 + - - +
107A VAL 3.3 6.6 + - - +
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Residues in contact with VAL 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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13A MET* 4.0 7.4 - - + -
42A HIS* 3.7 23.1 - - - +
43A ILE 3.1 8.8 + - - +
44A ASP* 3.7 16.8 - - - +
45A CYS* 2.9 32.1 + - - +
74A PHE* 3.9 22.4 - - + -
75A ILE* 1.4 78.7 - - - +
77A SER* 1.3 66.4 + - - +
78A LYS* 5.1 0.4 - - + -
107A VAL* 3.4 18.6 - - + +
109A LEU* 3.7 31.9 - - + -
182A THR* 6.2 0.4 - - + -
184A GLN* 4.7 1.1 - - - +
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Residues in contact with SER 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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45A CYS* 3.4 7.4 - - - -
46A ALA* 3.5 4.9 - - - -
47A TYR 3.9 1.9 + - - -
52A GLU* 2.4 29.6 + - - -
76A VAL* 1.3 77.5 - - - +
78A LYS* 1.3 73.4 + - - +
96A THR* 3.4 23.7 + - - +
100A LEU* 4.4 0.9 - - - -
105A LEU* 3.8 15.5 - - - +
107A VAL 3.2 7.1 + - - +
108A TYR* 3.5 7.6 - - - -
109A LEU* 2.9 22.0 + - - +
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Residues in contact with LYS 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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44A ASP* 2.7 32.6 + - - -
45A CYS 2.8 21.7 + - - +
46A ALA* 4.2 2.6 - - + +
47A TYR* 3.8 22.9 + - - +
49A TYR* 2.8 21.1 + - - -
76A VAL* 5.1 0.2 - - + -
77A SER* 1.3 86.8 + - - +
79A LEU* 1.3 60.8 - - - +
80A TRP* 3.8 2.6 + - - +
108A TYR* 3.6 10.1 + - - -
109A LEU* 3.1 24.7 - - + +
111A HIS* 3.6 45.7 + - + +
160A SER* 4.9 0.7 - - - +
184A GLN* 3.2 29.6 - - - +
401A NAP 3.8 3.6 - - - +
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Residues in contact with LEU 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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47A TYR* 5.8 0.4 - - - -
78A LYS* 1.3 70.0 - - - +
80A TRP* 1.3 66.8 + - - +
81A PRO* 3.9 1.2 - - - +
83A PHE* 3.8 27.8 - - + +
84A PHE* 3.9 13.9 - - + -
89A VAL* 3.9 20.4 - - + +
92A ALA* 4.0 11.0 - - + -
108A TYR* 3.5 28.7 - - + +
109A LEU 2.7 14.5 + - - +
110A ILE* 3.9 3.9 - - + -
111A HIS* 3.0 28.4 + - - +
141A ALA* 3.8 22.2 - - + -
145A MET* 3.8 26.2 - - + -
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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