Contacts of the helix formed by residues 325 - 336 (chain A) in PDB entry 4IX8
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 ASN 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TRP 4.5 14.4 - - - +
294A ARG* 5.2 0.9 + - + +
324A VAL* 1.3 75.8 - - + +
326A SER* 1.3 62.9 + - - +
327A ILE* 3.2 12.1 + - - +
328A CYS* 2.9 44.1 + - + +
329A GLN* 3.3 22.2 + - - +
97B MET* 5.7 4.2 - - - +
292B GLY 3.4 6.5 - - - -
293B TRP* 3.1 34.3 + - - +
294B ARG* 3.7 8.1 - - + +
295B VAL* 5.7 0.8 - - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 2.8 31.0 + - - +
108A GLY 3.7 15.2 + - - -
110A PRO* 4.6 9.0 - - - -
324A VAL 3.1 4.6 + - - -
325A ASN* 1.3 72.2 - - - +
327A ILE* 1.3 64.7 + - - +
329A GLN* 3.5 8.7 + - - +
330A GLU* 3.3 23.0 + - - +
292B GLY* 2.8 32.2 + - - -
293B TRP* 3.7 4.2 + - - -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.8 35.7 - - + +
100A VAL* 3.6 20.4 - - + +
101A VAL* 3.9 24.7 - - + -
106A PHE* 3.4 19.7 - - + +
107A ASN* 3.4 16.8 - - - +
325A ASN* 3.2 9.7 + - - +
326A SER* 1.3 78.5 - - - +
328A CYS* 1.3 58.5 + - - +
330A GLU 3.4 0.2 + - - -
331A ALA* 2.9 26.7 + - - +
97B MET* 4.1 17.0 - - + -
293B TRP* 3.7 20.4 - - + +
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Residues in contact with CYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.6 35.0 - - - -
293A TRP* 3.8 35.4 - - + -
295A VAL* 3.7 21.5 - - + -
325A ASN* 2.9 24.7 + - - +
326A SER 3.4 0.2 - - - -
327A ILE* 1.3 73.3 - - - +
329A GLN* 1.3 56.5 + - - +
332A ILE* 2.8 42.7 + - + +
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Residues in contact with GLN 329 (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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110A PRO* 3.9 18.6 - - - +
114A GLY* 3.4 9.1 - - - -
115A ALA* 2.8 39.1 + - + +
117A ASN* 5.5 1.1 - - - -
118A LEU* 3.8 26.3 - - + +
146A ILE* 3.7 20.3 - - + +
295A VAL* 5.0 2.2 - - + -
324A VAL* 2.8 40.7 + - + +
325A ASN 3.3 11.6 + - - +
326A SER* 3.9 6.8 - - - +
327A ILE 3.3 0.2 - - - -
328A CYS* 1.3 77.9 - - - +
330A GLU* 1.3 57.6 + - - +
332A ILE* 3.8 1.2 - - - -
333A ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 330 (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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100A VAL* 3.5 22.7 - - + -
106A PHE* 3.5 44.7 - - + -
117A ASN* 2.6 34.1 + - - +
326A SER 3.3 10.5 + - - +
327A ILE 4.0 2.2 - - - +
329A GLN* 1.3 75.3 - - - +
331A ALA* 1.3 67.4 + - - +
333A ALA* 3.0 4.3 + - - +
334A ARG* 2.7 55.3 + - - +
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Residues in contact with ALA 331 (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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93A VAL* 4.4 3.4 - - + +
96A ALA* 4.0 6.7 - - + +
97A MET* 3.5 47.1 - - + +
100A VAL* 3.9 8.2 - - + +
327A ILE 2.9 18.6 + - - +
328A CYS 3.2 2.4 + - - +
330A GLU* 1.3 75.1 - - - +
332A ILE* 1.3 61.4 - - + +
334A ARG* 3.3 11.5 + - - +
335A THR* 2.9 23.1 + - - +
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Residues in contact with ILE 332 (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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93A VAL* 4.9 13.0 - - + -
118A LEU* 3.8 17.7 - - + -
284A THR* 4.0 34.8 - - + +
288A GLN* 5.0 4.5 - - - +
293A TRP* 4.8 10.1 - - + -
295A VAL* 4.0 29.4 - - + -
297A TRP* 5.0 3.8 - - + -
328A CYS* 2.8 30.1 + - + +
329A GLN* 4.1 2.7 - - - +
331A ALA* 1.3 70.3 - - + +
333A ALA* 1.3 62.8 + - - +
334A ARG 3.1 1.8 - - - -
335A THR* 3.8 5.6 - - - +
336A LEU* 2.9 47.4 + - + +
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Residues in contact with ALA 333 (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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117A ASN* 3.7 34.3 - - - +
118A LEU* 3.9 19.7 - - - +
121A VAL* 3.6 24.1 - - + +
329A GLN 2.9 19.8 + - - +
330A GLU* 3.4 6.3 - - - +
332A ILE* 1.3 79.1 - - - +
334A ARG* 1.3 59.0 + - - +
335A THR 3.6 0.2 + - - -
336A LEU 4.7 0.7 + - - -
337A LEU* 5.6 2.4 + - - +
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Residues in contact with ARG 334 (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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96A ALA* 4.5 9.6 - - + +
99A ASP* 3.9 22.4 + - - +
100A VAL* 3.6 26.8 - - - +
103A SER* 5.2 4.0 + - - -
106A PHE* 3.5 24.0 - - - -
330A GLU* 2.7 40.0 + - - +
331A ALA 3.6 7.9 - - - +
332A ILE 3.1 0.4 - - - -
333A ALA* 1.3 80.2 - - - +
335A THR* 1.3 65.3 + - + +
337A LEU 5.4 0.4 - - - -
338A LYS* 3.7 27.2 + - - +
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Residues in contact with THR 335 (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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92A ILE* 3.5 40.4 - - + +
93A VAL* 3.4 25.6 - - - +
96A ALA* 3.5 18.4 - - + -
288A GLN* 5.2 0.7 + - - -
331A ALA 2.9 11.7 + - - +
332A ILE* 3.2 5.9 + - - -
334A ARG* 1.3 85.6 - - + +
336A LEU* 1.3 59.2 + - - +
337A LEU 3.1 2.9 - - - -
338A LYS* 2.7 27.0 + - + -
339A CYS* 3.1 17.3 + - - -
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Residues in contact with LEU 336 (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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121A VAL* 3.8 20.4 - - + -
122A VAL* 4.1 19.5 - - + -
125A TYR* 3.7 47.9 - - + -
128A ARG* 4.7 3.8 + - - -
284A THR* 3.9 21.8 - - + -
287A TYR* 3.4 26.9 + - - +
288A GLN* 4.2 7.6 - - - +
297A TRP* 4.2 9.4 - - + -
332A ILE* 2.9 26.3 + - + +
333A ALA 4.7 0.6 + - - -
334A ARG 3.9 0.2 - - - -
335A THR* 1.3 78.6 + - - +
337A LEU* 1.3 57.9 + - - +
338A LYS 3.7 0.2 + - - -
339A CYS* 4.2 9.0 + - - +
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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