Contacts of the helix formed by residues 36 - 45 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 1.3 89.5 - - - +
37A VAL* 1.3 65.3 + - + +
38A GLU 4.5 0.2 - - - +
39A PRO* 3.4 18.0 - - + +
40A LEU* 3.3 12.5 - - - +
91A GLU* 5.6 1.6 - - - +
94A ALA* 3.4 33.6 + - - +
96A THR 2.8 19.0 + - - +
165A ARG* 3.8 26.4 + - - +
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Residues in contact with VAL 37 (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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36A ASP* 1.3 74.0 - - + +
38A GLU* 1.3 72.7 + - + +
40A LEU* 3.4 16.1 + - - +
41A MET* 3.6 15.8 + - + +
62A PRO* 4.3 23.3 - - + -
65A LEU* 5.4 5.4 - - + +
94A ALA 4.3 2.1 + - - +
95A LYS* 6.3 0.9 - - + -
96A THR* 3.6 27.9 + - + +
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Residues in contact with GLU 38 (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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36A ASP* 4.5 0.6 - - + +
37A VAL* 1.3 85.1 - - + +
39A PRO* 1.3 69.2 - - + +
40A LEU 3.0 3.5 + - - -
41A MET* 3.0 27.8 + - - +
42A HIS* 3.4 23.6 + - - -
167A TYR* 3.0 26.5 - - - +
221B LYS* 5.5 4.5 - - - -
244B THR* 2.8 48.2 + - - +
245B GLU* 4.1 4.9 + - - +
270B SAM 5.4 7.4 - - - +
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Residues in contact with PRO 39 (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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34A ILE* 3.6 13.0 - - + -
35A GLU 3.2 20.6 - - - +
36A ASP* 3.4 22.4 - - + +
38A GLU* 1.3 96.1 - - + +
40A LEU* 1.3 56.2 + - - +
42A HIS* 3.8 1.4 + - - +
43A SER* 2.6 34.0 + - - -
165A ARG* 3.3 22.4 - - + +
166A GLY 4.0 9.8 - - - +
167A TYR* 3.5 25.5 - - + +
170A SER* 4.7 0.5 + - - -
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Residues in contact with LEU 40 (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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34A ILE* 3.7 26.2 - - + +
36A ASP 3.3 16.2 - - - +
37A VAL 3.5 7.2 - - - +
38A GLU 3.0 0.6 + - - -
39A PRO* 1.3 75.1 - - - +
41A MET* 1.3 66.5 + - - +
43A SER* 3.1 5.0 + - - -
44A ILE* 3.0 31.9 + - + +
50A PHE* 3.4 30.7 - - + -
53A VAL* 4.4 6.3 - - + -
65A LEU* 4.2 17.7 - - + -
96A THR* 3.4 40.6 - - + +
97A PHE* 3.9 7.6 - - - +
98A GLY* 4.1 5.8 - - - +
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Residues in contact with MET 41 (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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37A VAL* 3.6 19.7 + - + +
38A GLU* 3.0 20.7 + - - +
40A LEU* 1.3 80.1 - - + +
42A HIS* 1.3 62.8 + - + +
44A ILE* 3.3 6.3 + - - +
45A ALA* 2.8 30.4 + - - +
64A GLU* 3.3 33.9 - - + +
65A LEU* 4.4 28.5 - - + -
68A LEU* 3.5 35.3 - - + +
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Residues in contact with HIS 42 (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 GLU* 3.4 25.1 + - - +
39A PRO 4.5 1.3 - - - +
40A LEU 3.4 0.2 - - - -
41A MET* 1.3 80.6 - - + +
43A SER* 1.3 63.2 + - - +
45A ALA* 3.3 18.1 + - + -
46A ALA* 3.4 17.3 + - - +
138A LEU* 4.4 16.4 - - + +
167A TYR* 3.9 22.0 - + + -
170A SER* 3.4 26.3 + - - +
242B SER* 5.1 1.0 + - - -
244B THR* 5.1 3.7 - - + +
245B GLU* 2.8 36.4 + - - -
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Residues in contact with SER 43 (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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34A ILE* 3.4 19.1 - - - +
39A PRO 2.6 22.8 + - - -
40A LEU 3.4 4.7 - - - -
42A HIS* 1.3 77.7 - - - +
44A ILE* 1.3 60.7 + - - +
46A ALA* 3.3 7.1 + - - +
47A GLY 3.5 0.3 + - - -
48A VAL* 3.1 38.0 + - - +
50A PHE* 3.6 22.0 - - - -
166A GLY 3.8 8.5 + - - -
169A PHE* 4.4 6.8 - - - +
170A SER* 4.0 5.9 + - - -
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Residues in contact with ILE 44 (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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40A LEU* 3.0 20.5 + - + +
41A MET* 3.9 5.2 - - - +
43A SER* 1.3 70.9 - - - +
45A ALA* 1.3 57.6 + - - +
46A ALA 3.0 10.9 + - - -
47A GLY* 3.8 7.8 + - - -
48A VAL 4.3 11.5 - - - +
50A PHE* 3.4 24.0 - - + -
53A VAL* 5.4 1.6 - - + -
65A LEU* 4.5 8.5 - - + -
68A LEU* 3.8 27.1 - - + +
69A CYS* 3.9 20.6 - - - -
72A GLN* 4.0 14.8 + - + +
74A ILE* 3.8 27.4 - - + -
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Residues in contact with ALA 45 (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 MET 2.8 19.4 + - - +
42A HIS* 3.5 19.3 - - + +
43A SER 3.2 0.8 - - - -
44A ILE* 1.3 75.7 - - - +
46A ALA* 1.3 57.7 + - - +
68A LEU* 5.4 9.2 - - + -
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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