Contacts of the helix formed by residues 397 - 405 (chain A) in PDB entry 4GL5
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 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A CYS* 3.7 11.3 - - + +
75A ASN* 3.7 33.7 + - - +
78A ASN* 2.9 27.7 + - - +
96A ILE* 5.8 0.4 - - + -
97A ILE 2.8 18.6 + - - +
98A SER* 3.9 4.8 - - - -
371A ASP* 3.7 14.7 - - - +
372A LEU* 4.5 5.2 - - - -
395A ILE* 3.5 3.5 + - + +
396A LEU* 1.3 69.1 - - - +
398A ILE* 1.3 61.0 + - - +
399A GLY* 2.9 5.0 + - - -
400A ARG* 2.9 28.2 + - - +
401A MET* 3.1 12.2 + - - +
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Residues in contact with ILE 398 (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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103A MET* 4.2 24.5 - - + -
107A MET* 5.3 3.8 - - - -
368A PRO* 6.1 0.7 - - + -
370A VAL 3.3 23.3 - - - +
371A ASP* 3.1 16.2 + - - +
372A LEU* 4.1 4.3 - - - +
373A VAL* 4.6 10.8 - - + -
396A LEU* 3.1 12.2 + - + +
397A ASN* 1.3 73.1 - - - +
399A GLY* 1.3 59.9 + - - +
400A ARG 3.3 0.2 - - - -
401A MET* 3.8 11.8 - - - +
402A HIS* 3.1 39.3 + - + +
428A GLN* 3.6 29.4 - - + +
429A PRO* 4.1 16.6 - - + +
600A HEM 4.7 10.3 - - + -
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Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 5.6 2.0 - - - -
365A ARG 4.9 3.5 - - - +
368A PRO* 4.5 13.0 - - - +
371A ASP* 2.8 32.0 + - - -
397A ASN* 2.9 2.0 + - - -
398A ILE* 1.3 79.3 - - - +
400A ARG* 1.3 57.3 + - - +
402A HIS* 3.9 13.8 + - - +
403A ARG* 4.3 16.5 + - - +
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Residues in contact with ARG 400 (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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75A ASN* 3.3 25.2 + - - +
78A ASN* 3.4 24.4 - - - +
79A ARG* 3.6 39.3 + - - +
83A GLU* 2.8 27.0 + - - -
98A SER* 4.0 5.2 - - - +
397A ASN* 2.9 22.8 + - - +
399A GLY* 1.3 72.6 - - - +
401A MET* 1.3 61.5 + - - +
402A HIS 3.1 2.0 - - - -
403A ARG* 2.9 25.4 + - - +
404A LEU* 3.2 36.3 + - + +
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Residues in contact with MET 401 (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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98A SER* 3.1 31.1 - - - +
100A SER* 3.7 24.7 - - - +
103A MET* 3.6 46.2 - - + -
397A ASN 3.1 14.6 + - - +
398A ILE* 3.8 9.9 - - + +
400A ARG* 1.3 77.4 - - - +
402A HIS* 1.3 78.1 + - + +
403A ARG 3.1 3.9 + - - -
404A LEU* 4.6 4.5 - - - +
405A GLU* 3.5 24.8 + - + +
426A TYR 3.4 29.1 - - - +
428A GLN* 4.3 2.2 - - + +
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Residues in contact with HIS 402 (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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364A MET 4.9 2.4 + - - -
365A ARG* 3.0 46.7 + - + +
368A PRO* 6.1 1.4 - - - +
398A ILE* 3.1 22.8 + - + +
399A GLY* 4.2 9.0 - - - +
400A ARG 3.1 1.2 - - - -
401A MET* 1.3 96.2 - - + +
403A ARG* 1.3 59.3 + - - +
405A GLU 4.9 1.3 - - - -
407A PHE* 3.8 16.7 - + - -
410A PRO* 4.7 1.0 - - - +
426A TYR 3.7 8.1 - - - -
427A PHE* 3.3 32.8 - + - -
428A GLN 3.1 42.4 + - - -
429A PRO* 4.0 6.3 - - + -
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Residues in contact with ARG 403 (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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365A ARG* 4.3 5.9 + - - +
366A TYR* 2.7 55.8 + - - -
367A GLN* 5.9 0.2 - - - +
399A GLY 4.3 13.9 + - - +
400A ARG* 2.9 10.8 + - + +
402A HIS* 1.3 86.7 - - + +
404A LEU* 1.3 70.9 + - + +
405A GLU 3.6 1.8 - - - -
410A PRO* 3.3 37.6 - - - +
411A ASN* 2.9 52.0 + - - +
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Residues in contact with LEU 404 (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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83A GLU* 2.8 37.0 - - + +
98A SER* 4.0 7.0 - - - +
400A ARG* 3.2 46.4 + - + +
401A MET* 3.7 2.9 + - - +
403A ARG* 1.3 90.5 - - + +
405A GLU* 1.3 70.5 + - - +
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Residues in contact with GLU 405 (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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98A SER 3.8 14.0 - - - +
99A LYS* 4.0 5.4 - - - +
100A SER* 2.9 43.6 + - - -
101A SER* 4.4 2.1 + - - -
401A MET* 3.5 16.0 + - + +
402A HIS 4.8 0.2 - - - +
403A ARG 4.7 2.9 - - - -
404A LEU* 1.3 89.6 + - - +
406A PHE* 1.3 59.9 + - + +
407A PHE* 2.5 31.2 + - - +
410A PRO* 5.4 0.9 - - - +
426A TYR* 4.4 15.7 - - + +
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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