Contacts of the strand formed by residues 3 - 8 (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 ILE 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 1.3 78.1 - - + +
4A ASP* 1.3 69.6 + - - +
5A ILE* 4.5 2.5 - - + +
68A VAL* 4.9 0.2 - - - -
69A THR* 5.6 0.7 - - - -
70A VAL* 3.4 35.7 - - + +
72A ALA* 5.4 1.3 - - + +
288A LEU* 3.3 24.5 + - - +
320A LYS 2.7 20.9 + - - +
321A ALA* 3.6 31.4 - - + +
324A ALA* 3.7 23.3 - - + +
325A LEU* 3.6 28.5 - - + -
328A LEU* 5.1 10.1 - - + -
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Residues in contact with ASP 4 (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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2A LYS 4.1 0.2 + - - -
3A ILE* 1.3 73.2 - - - +
5A ILE* 1.3 61.7 + - - +
6A HIS 3.1 16.8 + - - +
7A SER* 4.0 8.6 - - - -
68A VAL* 4.2 17.5 - - + +
70A VAL 2.9 14.3 + - - +
71A GLN* 3.5 9.4 + - + -
72A ALA* 3.0 26.7 + - - +
288A LEU* 3.5 5.4 - - + -
289A GLY* 3.2 2.3 - - - -
290A THR* 2.8 56.1 + - - +
292A TYR* 4.2 2.6 - - - +
301A PRO* 6.0 0.2 - - + -
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Residues in contact with ILE 5 (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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3A ILE* 3.9 1.9 + - + +
4A ASP* 1.3 72.9 - - - +
6A HIS* 1.3 61.8 + - + +
7A SER 4.0 1.5 + - - -
72A ALA* 3.9 18.1 - - + +
114A LEU* 4.1 12.2 - - + +
172A PHE* 4.4 17.1 - - + -
221A CYS* 4.8 1.3 - - - -
265A ASP* 3.9 26.0 - - + -
287A ILE* 3.4 29.6 - - + -
288A LEU 2.9 19.1 + - - +
289A GLY* 3.9 0.9 - - - -
324A ALA* 4.6 5.2 - - + -
327A PHE* 4.1 19.7 - - + -
328A LEU* 3.7 41.1 - - + -
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Residues in contact with HIS 6 (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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4A ASP* 3.1 8.4 + - - +
5A ILE* 1.3 80.2 - - + +
7A SER* 1.3 64.8 + - - +
8A HIS* 3.4 13.7 - + - -
74A SER* 5.7 0.2 - - - -
172A PHE* 3.9 16.3 - + + -
174A HIS* 3.1 15.1 + + - -
223A ALA* 4.3 3.6 - - + -
224A HIS* 3.7 24.0 - + - -
265A ASP* 2.9 21.4 + - - +
267A LEU* 4.0 6.2 - - + +
289A GLY* 3.9 16.8 - - - -
290A THR 3.9 0.4 - - - +
291A ASP* 2.9 33.4 + - + -
401A ZN 2.2 36.7 - - - -
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Residues in contact with SER 7 (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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4A ASP* 4.0 13.2 - - - -
5A ILE 4.1 0.2 + - - -
6A HIS* 1.3 82.2 - - - +
8A HIS* 1.3 63.2 + - - +
59A ARG* 3.2 17.6 + - - -
71A GLN* 3.5 18.2 - - - +
72A ALA 3.4 17.1 + - - +
73A LEU* 3.6 2.9 - - - +
74A SER* 2.9 28.3 + - - -
292A TYR* 3.4 17.7 - - - -
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Residues in contact with HIS 8 (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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6A HIS* 3.3 13.2 + + - -
7A SER* 1.3 75.0 - - - +
9A ILE* 1.3 61.6 - - - +
53A CYS* 4.6 1.1 - - - +
59A ARG* 2.8 22.0 + - - -
74A SER* 3.0 18.6 + - - +
75A THR 2.8 27.6 + - - -
76A VAL* 4.0 12.6 - - + -
77A PRO* 3.9 7.3 - - + +
142A GLN* 3.2 20.8 + - - -
174A HIS* 3.4 3.3 + - - -
291A ASP* 3.6 6.3 + - - -
292A TYR 3.0 9.3 + - - +
293A PRO* 3.5 9.9 - - - +
294A PHE* 3.8 27.9 - + + -
401A ZN 2.4 37.6 - - - -
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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