Contacts of the helix formed by residues 36 - 46 (chain B) in PDB entry 3GYQ
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 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLU* 1.3 86.1 - - - +
37B VAL* 1.3 66.5 + - + +
38B GLU 3.5 0.2 - - - -
39B PRO* 3.4 14.9 - - + +
40B LEU* 3.2 21.2 + - - +
91B GLU* 5.2 5.4 - - - +
93B LYS 4.6 1.9 - - - +
94B ALA* 3.0 29.6 - - - +
96B THR* 2.6 20.9 + - - -
165B ARG* 4.8 16.1 + - - +
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Residues in contact with VAL 37 (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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36B ASP* 1.3 71.4 - - + +
38B GLU* 1.3 74.8 + - + +
40B LEU* 3.1 7.6 + - - +
41B MET* 2.7 54.3 + - + +
62B PRO* 3.9 35.7 - - + -
64B GLU* 4.8 5.4 - - - +
65B LEU* 4.0 15.0 - - + -
96B THR* 4.3 7.0 - - + -
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Residues in contact with GLU 38 (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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221A LYS* 6.5 1.1 - - - -
244A THR* 2.8 47.5 + - + +
245A GLU* 5.1 2.9 - - - -
36B ASP* 4.7 0.2 - - - +
37B VAL* 1.3 91.5 - - + +
39B PRO* 1.3 68.2 - - + +
41B MET* 3.2 10.0 + - - +
42B HIS* 2.9 55.6 + - + +
64B GLU* 4.4 11.6 - - - +
167B TYR* 3.1 22.4 - - - +
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.8 6.1 - - + -
35B GLU 3.2 20.9 - - - +
36B ASP* 3.4 21.5 - - + +
38B GLU* 1.3 95.0 - - + +
40B LEU* 1.3 52.8 + - - +
42B HIS 3.9 0.2 - - - -
43B SER* 2.6 38.1 + - - -
165B ARG* 3.4 19.7 - - - +
166B GLY* 3.6 20.0 - - - +
167B TYR* 3.5 24.9 - - + +
170B SER* 4.1 1.4 + - - -
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Residues in contact with LEU 40 (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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34B ILE* 3.5 22.7 - - + +
36B ASP 3.2 15.2 + - - +
37B VAL* 3.1 9.1 + - - +
39B PRO* 1.3 77.7 - - - +
41B MET* 1.3 65.8 + - - +
43B SER* 3.3 2.2 + - - -
44B ILE* 2.9 34.3 + - + +
50B PHE* 3.4 33.2 - - + -
53B VAL* 4.2 10.3 - - + -
65B LEU* 4.1 16.2 - - + -
96B THR* 3.5 32.1 - - + -
97B PHE* 3.8 16.4 - - - -
98B GLY* 3.8 6.1 - - - +
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Residues in contact with MET 41 (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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37B VAL* 2.7 35.5 + - + +
38B GLU* 3.6 17.3 - - - +
40B LEU* 1.3 72.4 - - - +
42B HIS* 1.3 59.7 + - + +
44B ILE* 3.5 2.6 + - - +
45B ALA* 3.1 27.8 + - - +
64B GLU* 3.8 34.3 - - + +
65B LEU* 3.6 36.6 - - - -
68B LEU* 3.8 26.4 - - + +
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Residues in contact with HIS 42 (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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242A SER* 4.9 4.0 + - - -
244A THR* 4.8 4.0 - - + -
245A GLU* 3.6 26.1 + - - -
38B GLU* 2.9 49.0 + - + +
41B MET* 1.3 75.7 - - + +
43B SER* 1.3 64.4 + - - +
45B ALA* 3.4 8.0 + - + +
46B ALA* 3.1 23.4 + - - +
138B LEU* 4.2 24.7 - - + +
167B TYR* 4.0 8.9 - + + -
170B SER* 3.2 26.9 + - - +
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Residues in contact with SER 43 (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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34B ILE* 3.3 21.0 - - - +
39B PRO 2.6 25.4 + - - -
40B LEU 3.5 4.5 - - - -
42B HIS* 1.3 74.0 - - - +
44B ILE* 1.3 66.1 + - - +
46B ALA* 2.9 12.5 + - - +
48B VAL* 3.1 32.9 + - - +
50B PHE* 3.7 21.1 - - - -
166B GLY 4.3 3.5 + - - -
169B PHE* 4.7 4.9 - - - +
170B SER* 3.8 9.2 + - - +
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Residues in contact with ILE 44 (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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40B LEU* 2.9 20.7 + - + +
43B SER* 1.3 74.6 - - - +
45B ALA* 1.3 62.5 + - - +
47B GLY* 3.0 14.7 + - - -
48B VAL 4.2 8.9 - - - +
50B PHE* 3.5 21.3 - - + -
53B VAL* 5.1 2.5 - - + -
65B LEU* 4.2 9.6 - - + -
68B LEU* 3.8 37.2 - - + -
69B CYS* 4.0 19.3 - - - -
72B GLN* 4.0 29.4 + - + +
74B ILE* 3.9 20.4 - - + -
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Residues in contact with ALA 45 (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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41B MET 3.1 18.6 + - - +
42B HIS* 3.6 11.0 - - + +
44B ILE* 1.3 76.7 - - - +
46B ALA* 1.3 58.9 + - - +
47B GLY* 3.2 1.5 + - - -
68B LEU* 4.9 4.2 - - + +
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Residues in contact with ALA 46 (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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42B HIS 3.1 15.8 + - - +
43B SER 2.9 6.5 + - - +
45B ALA* 1.3 75.3 - - - +
47B GLY* 1.3 58.6 + - - +
48B VAL* 3.3 4.2 + - + +
114B ARG* 5.8 5.6 - - - +
169B PHE 3.5 24.9 - - - +
170B SER 4.0 12.3 - - - +
171B LEU* 5.5 0.7 - - - -
172B PRO* 6.5 0.2 - - + -
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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