Contacts of the strand formed by residues 37 - 44 (chain E) in PDB entry 4GG6
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 ASP 37 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E THR 4.8 1.2 - - - +
28E ILE* 3.7 16.7 - - + +
29E SER* 3.1 40.4 + - - +
30E GLY 3.4 0.6 - - - -
36E THR* 1.3 79.8 - - - +
38E TYR* 1.3 64.1 + - - +
57E LEU* 3.4 4.0 - - - +
84E ARG* 2.7 31.5 + - - -
106E LEU* 4.4 14.2 - - + +
107E ARG 3.3 4.9 - - - +
108E ASP* 3.5 26.0 + - - +
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Residues in contact with TYR 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU 4.0 2.0 + - - -
70D ARG* 3.9 15.1 + - - -
73D ALA* 3.4 26.2 - - - +
77D THR* 4.7 8.9 - - + +
36E THR 4.4 1.1 - - - -
37E ASP* 1.3 74.4 - - - +
39E ILE* 1.3 62.6 + - - +
40E HIS* 3.7 6.5 - - - +
55E HIS* 3.6 25.1 - + - -
56E GLY* 3.3 19.5 - - - -
57E LEU* 3.6 31.1 - - + +
105E ILE 3.6 0.3 - - - +
106E LEU* 3.4 8.5 - - - +
107E ARG 2.6 35.9 + - - +
109E GLY* 3.6 23.8 - - - -
112F GLY 3.7 13.7 - - - +
113F THR* 3.5 21.4 - - + +
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Residues in contact with ILE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 3.4 28.9 - - + +
28E ILE* 3.7 19.7 - - + -
37E ASP 5.3 0.2 - - - +
38E TYR* 1.3 76.3 - - - +
40E HIS* 1.3 63.9 + - - +
41E TRP* 3.9 17.3 - - + +
55E HIS* 3.0 6.1 - - - +
56E GLY 2.7 40.7 + - - +
57E LEU 5.1 3.1 - - - +
78E LEU* 4.1 9.7 - - + +
80E ILE* 3.6 35.9 - - + -
87E SER* 3.7 18.6 - - - +
104E CYS* 4.3 7.6 - - - -
105E ILE 3.5 6.1 - - - +
106E LEU* 3.8 6.3 - - + -
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Residues in contact with HIS 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E TYR* 3.7 13.7 - - + +
39E ILE* 1.3 79.7 - - - +
41E TRP* 1.3 66.3 + - - +
42E TYR* 4.3 22.3 - - + -
52E TYR* 4.6 2.4 - - - -
54E ILE 3.7 3.4 - - - -
55E HIS* 3.5 22.8 - + + +
103E TYR 3.6 1.0 - - - +
104E CYS* 3.4 4.7 - - - -
105E ILE* 2.8 52.5 + - + +
107E ARG* 3.7 28.6 + - + +
112F ALA 2.7 50.8 + - - -
113F THR 4.2 0.4 - - - -
114F TYR 4.3 6.4 + - - -
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Residues in contact with TRP 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 3.4 28.7 - - - -
21E LEU* 3.7 33.0 - - + -
22E PRO 3.8 4.7 - - - -
23E CYS* 3.3 28.9 - - + -
39E ILE* 3.9 8.6 - - + +
40E HIS* 1.3 78.8 - - - +
42E TYR* 1.3 66.8 + - - +
53E VAL* 2.9 27.6 + - + +
54E ILE* 3.0 19.9 + - + +
78E LEU* 3.6 30.8 - - + +
87E SER* 3.8 9.4 + - - -
89E LEU* 3.6 49.1 - - + -
102E TYR* 4.2 13.5 - + + -
103E TYR 3.3 16.6 - - - -
104E CYS* 3.7 4.7 - - + -
122E THR* 6.0 0.2 - - - -
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Residues in contact with TYR 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E HIS* 4.3 20.0 - - + -
41E TRP* 1.3 81.8 - - - +
43E ARG* 1.3 62.4 + - - +
50E PRO* 4.7 2.7 - - + -
51E GLU* 3.4 23.3 - - - -
52E TYR* 3.5 33.7 - + + -
53E VAL* 4.0 3.1 - - - -
102E TYR* 3.3 5.6 - - - +
103E TYR* 2.8 38.0 + - + +
105E ILE* 5.4 0.2 - - + -
107E ARG* 4.1 7.9 + - - -
118E PHE* 3.4 39.0 - + + -
114F TYR 4.2 1.0 + - - -
115F GLU* 3.5 8.1 - - - -
116F GLN* 2.8 47.2 + - - +
118F PHE* 4.1 14.1 - + - -
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Residues in contact with ARG 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E TYR* 1.3 74.8 - - - +
44E GLN* 1.3 62.8 + - - +
45E LEU* 4.4 19.5 - - - +
50E PRO* 3.1 4.8 - - - +
51E GLU* 2.7 73.3 + - + +
52E TYR 5.9 0.2 - - - -
53E VAL* 3.8 11.2 - - + +
75E MET* 6.2 3.3 - - - -
97E ARG* 3.6 18.4 + - - +
98E ASP* 2.9 28.1 + - - +
100E ALA* 4.6 4.3 - - + -
101E VAL 3.0 7.2 - - - +
102E TYR* 3.5 40.1 + - + -
103E TYR* 4.8 0.9 - - - -
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Residues in contact with GLN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ARG* 1.3 78.9 - - - +
45E LEU* 1.3 66.6 + - - +
46E PRO* 3.6 4.2 + - - +
48E GLN 3.6 23.8 + - - +
49E GLY 4.3 0.9 - - - -
50E PRO* 3.7 24.4 - - + +
51E GLU* 5.7 0.2 - - - -
100E ALA* 3.4 3.3 - - - +
101E VAL* 2.8 36.7 + - + +
103E TYR* 2.6 41.0 + - + +
44F GLN* 2.7 33.7 + - - +
50F LEU* 4.0 1.4 - - - +
101F LEU* 5.3 0.6 - - - +
103F PHE* 3.8 15.2 - - - -
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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