Contacts of the strand formed by residues 36 - 41 (chain A) in PDB entry 4IGM
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 GLU 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A HIS* 4.3 12.3 + - - +
32A HIS* 4.2 15.9 + - + -
33A SER* 3.3 21.6 + - - +
34A LYS 3.9 9.8 - - - +
35A GLY* 1.3 80.5 - - - +
37A ALA* 1.3 62.1 + - - +
38A LYS* 4.9 2.3 - - - -
48A VAL* 3.4 34.1 - - + +
49A VAL 3.4 7.6 - - - +
50A ARG* 4.4 5.2 + - + +
54A TRP* 4.5 8.0 - - - -
312D ASP* 3.6 32.0 - - - +
313D GLU* 4.5 4.9 + - - +
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Residues in contact with ALA 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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29A LEU* 3.6 26.7 - - + -
30A GLN 3.3 13.9 - - - +
31A HIS* 3.8 16.8 - - + +
32A HIS* 5.1 0.9 - - - -
36A GLU* 1.3 76.3 - - - +
38A LYS* 1.3 65.2 + - - +
39A LEU 4.0 0.2 + - - -
48A VAL* 3.4 4.9 - - - +
49A VAL* 2.6 39.3 + - + +
54A TRP* 4.1 9.4 - - - +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN 3.5 1.7 - - - +
29A LEU* 3.4 5.1 - - - -
30A GLN* 2.7 53.9 + - - +
32A HIS* 3.7 39.9 - - + +
36A GLU* 4.9 2.7 - - - -
37A ALA* 1.3 75.2 - - - +
39A LEU* 1.3 59.6 + - - +
40A LEU* 3.8 1.9 + - + -
45A VAL* 3.6 42.6 - - + +
47A ARG 3.7 4.0 - - - -
48A VAL* 3.5 27.1 - - - +
313D GLU* 4.2 27.6 + - - +
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Residues in contact with LEU 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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10A LEU* 3.7 25.1 - - + -
14A TRP* 3.9 8.1 - - + -
27A VAL* 3.8 19.5 - - + -
28A GLN 3.3 2.7 - - - +
29A LEU* 3.3 25.6 - - + -
37A ALA 4.0 0.6 + - - -
38A LYS* 1.3 71.9 - - - +
40A LEU* 1.3 59.2 + - - +
45A VAL* 3.5 3.3 - - - -
46A PHE* 2.9 54.5 + - + -
47A ARG* 2.9 34.4 + - + +
49A VAL* 4.6 8.7 - - + -
76A VAL* 5.0 6.1 - - + -
78A VAL* 4.7 10.5 - - + -
294A PHE* 6.1 0.4 - - + -
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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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26A TRP 3.8 1.2 - - - +
27A VAL* 3.2 4.0 - - - -
28A GLN* 2.9 47.7 + - + +
30A GLN* 3.1 48.5 - - + +
38A LYS* 4.6 2.7 - - + -
39A LEU* 1.3 75.2 - - - +
41A LYS* 1.3 61.3 + - - +
42A ASP* 4.2 1.3 - - - +
43A GLY 4.7 11.7 - - - +
44A LYS 3.3 15.9 - - - +
45A VAL* 4.0 22.0 - - + +
46A PHE* 4.1 2.5 - - - -
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Residues in contact with LYS 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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25A GLY* 3.8 22.7 - - - +
26A TRP 3.8 4.7 - - - +
27A VAL* 4.4 7.2 - - + -
40A LEU* 1.3 73.2 - - - +
42A ASP* 1.3 76.9 + - - +
43A GLY 3.1 2.3 + - - -
44A LYS* 3.2 15.9 + - - +
46A PHE* 3.7 22.4 - - + -
78A VAL* 3.8 28.6 - - - +
180A MET* 5.8 5.9 - - - +
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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