Contacts of the strand formed by residues 37 - 44 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G THR 4.9 1.4 - - - +
28G ILE* 3.7 14.7 - - + +
29G SER* 3.1 39.7 + - - +
30G GLY 3.4 0.8 - - - -
36G THR* 1.3 79.3 - - - +
38G TYR* 1.3 64.7 - - - +
57G LEU* 3.4 4.3 - - - +
84G ARG* 2.7 31.0 + - - -
106G LEU* 4.3 17.0 - - + +
107G ARG 3.3 5.3 - - - +
108G ASP* 3.5 25.1 + - - +
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Residues in contact with TYR 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU 4.4 0.7 + - - -
70B ARG* 4.0 17.7 + - + -
73B ALA* 3.1 29.6 - - - +
77B THR* 4.6 9.9 - - + -
36G THR 4.4 0.9 - - - -
37G ASP* 1.3 75.4 - - - +
39G ILE* 1.3 61.8 + - - +
40G HIS* 3.7 17.3 - - + +
55G HIS* 3.6 28.9 - + - -
56G GLY* 3.3 20.6 - - - +
57G LEU* 3.7 29.8 - - + +
105G ILE 3.6 0.2 - - - +
106G LEU* 3.4 7.4 - - - +
107G ARG* 2.5 36.4 + - + +
109G GLY* 3.6 29.8 - - - +
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Residues in contact with ILE 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G HIS* 3.5 29.8 - - + +
28G ILE* 3.7 23.8 - - + -
38G TYR* 1.3 74.3 - - - +
40G HIS* 1.3 62.9 + - - +
41G TRP* 3.9 18.4 - - + +
55G HIS* 3.0 6.2 - - - +
56G GLY 2.8 40.0 + - - +
57G LEU 5.1 2.2 - - - +
78G LEU* 4.1 8.9 - - + +
80G ILE* 3.7 36.1 - - + -
84G ARG* 5.6 0.4 - - - +
87G SER* 3.7 18.6 - - - +
104G CYS* 4.3 7.4 - - - -
105G ILE 3.5 5.8 - - - +
106G LEU* 3.8 7.9 - - + -
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Residues in contact with HIS 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G TYR* 3.7 24.2 - - + +
39G ILE* 1.3 81.6 - - - +
41G TRP* 1.3 65.1 + - - +
42G TYR* 4.3 24.3 + - + -
52G TYR* 4.7 3.1 - + - -
54G ILE 3.7 2.9 - - - -
55G HIS* 3.5 27.3 - + + +
103G TYR 3.6 0.5 - - - +
104G CYS* 3.4 5.4 - - - +
105G ILE* 2.7 51.4 + - + +
107G ARG* 3.7 44.7 + - + +
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Residues in contact with TRP 41 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G GLN* 3.5 23.3 - - - -
21G LEU* 3.7 33.7 - - + -
22G PRO 3.9 4.9 - - - -
23G CYS* 3.4 32.8 - - + -
39G ILE* 3.9 8.8 - - + +
40G HIS* 1.3 78.7 - - - +
42G TYR* 1.3 66.0 + - - +
53G VAL* 2.8 27.0 + - + +
54G ILE* 2.9 20.4 + - + +
78G LEU* 3.6 30.9 - - + +
87G SER* 3.9 9.6 + - - -
89G LEU* 3.5 49.4 - - + -
102G TYR* 4.2 13.0 - - + -
103G TYR 3.3 17.0 - - - -
104G CYS* 3.7 5.4 - - + -
122G THR* 6.0 0.2 - - - -
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Residues in contact with TYR 42 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40G HIS* 4.3 21.1 + - + -
41G TRP* 1.3 84.0 - - - +
43G ARG* 1.3 62.5 + - - +
50G PRO* 4.7 5.6 - - + -
51G GLU* 3.4 13.2 - - - -
52G TYR* 3.4 55.3 - + + +
53G VAL* 3.9 2.9 - - - -
101G VAL 3.7 0.2 - - - +
102G TYR* 3.3 5.9 - - - +
103G TYR* 2.8 37.1 + - + +
105G ILE* 5.4 0.4 - - + -
107G ARG* 4.1 15.5 + - - -
118G PHE* 3.5 44.4 - + + -
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G TYR* 1.3 74.3 - - - +
44G GLN* 1.3 60.2 + - - +
45G LEU* 4.4 19.3 - - - +
50G PRO* 3.1 5.4 - - - +
51G GLU* 2.8 74.1 + - + +
52G TYR 5.9 0.2 - - - -
53G VAL* 3.7 10.9 - - + +
75G MET* 6.3 2.7 - - - -
91G LEU* 6.4 0.4 - - - +
97G ARG* 3.6 18.8 + - - +
98G ASP* 2.8 28.9 + - - +
100G ALA* 4.6 4.3 - - + -
101G VAL 3.0 7.6 - - - +
102G TYR* 3.6 38.6 + - + -
103G TYR* 4.8 1.3 - - - -
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ARG* 1.3 76.7 - - - +
45G LEU* 1.3 67.5 + - - +
46G PRO* 3.6 4.6 + - - +
48G GLN 3.6 24.3 + - - +
49G GLY* 3.8 1.3 - - - -
50G PRO* 3.7 30.4 - - + +
51G GLU* 5.7 0.4 - - - -
100G ALA* 3.3 3.5 - - - +
101G VAL* 2.8 36.6 + - + +
103G TYR* 2.6 42.3 + - + +
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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