Contacts of the strand formed by residues 432 - 438 (chain C) in PDB entry 3GXM
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 GLN 432 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LYS* 3.6 42.0 + - + +
75C PHE 2.6 28.5 + - - +
76C GLN 3.4 4.9 - - - +
77C LYS* 3.8 30.2 - - + +
430C GLY 3.3 2.8 + - - +
431C SER* 1.3 75.2 - - - +
433C ARG* 1.3 68.4 + - - +
434C VAL* 3.7 5.4 - - + +
449C LEU* 4.1 2.9 - - - -
450C MET* 2.6 42.6 + - + +
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Residues in contact with ARG 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 2.7 76.8 + - - +
76C GLN* 2.9 35.0 + - - +
78C VAL* 5.7 0.2 - - + -
371C LEU* 3.1 30.0 + - + +
372C LEU* 3.3 42.9 + - - +
374C HIS* 5.5 4.6 + - - +
432C GLN* 1.3 72.1 - - - +
434C VAL* 1.3 71.7 + - - +
435C GLY* 5.1 2.4 - - - -
436C LEU* 5.3 2.4 + - - +
447C VAL* 3.9 13.8 - - + +
448C ALA 3.5 13.5 - - - +
449C LEU* 3.9 14.0 - - + +
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Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 3.8 27.6 - - + -
70C GLN 3.9 5.4 - - - +
71C PRO* 4.0 15.3 - - + +
73C GLN 3.2 12.6 - - - +
74C LYS* 4.2 11.4 - - + +
75C PHE* 3.9 6.1 - - - -
432C GLN* 3.7 11.4 - - + +
433C ARG* 1.3 93.3 + - - +
435C GLY* 1.3 66.5 + - - +
436C LEU* 3.5 2.8 + - - +
448C ALA* 3.2 28.4 + - - +
449C LEU* 4.1 8.3 - - - -
450C MET* 4.1 22.0 - - + +
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Residues in contact with GLY 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 3.5 9.2 - - - +
70C GLN* 2.7 36.2 + - - -
73C GLN* 3.0 39.1 + - - -
75C PHE* 3.8 6.0 - - - -
433C ARG* 5.1 1.3 - - - -
434C VAL* 1.3 76.3 - - - +
436C LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.9 26.3 - - + +
68C THR 3.4 22.0 - - - +
69C LEU* 3.8 7.9 - - - +
73C GLN* 4.5 0.8 + - - -
433C ARG* 5.3 3.9 + - - +
434C VAL 3.5 2.7 + - - +
435C GLY* 1.3 74.7 - - - +
437C VAL* 1.3 60.9 + - - +
438C ALA* 4.1 1.2 + - - +
446C ALA* 3.9 25.4 - - + +
447C VAL* 3.8 26.2 - - - +
448C ALA* 3.7 17.7 - - + +
458C VAL* 3.9 21.1 - - + -
472C ILE* 4.6 4.7 - - + -
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU 3.4 2.3 - - - +
67C LEU* 3.3 6.8 - - - -
68C THR* 2.9 39.1 + - - +
70C GLN* 3.6 29.4 - - + +
73C GLN* 3.9 12.3 - - - +
436C LEU* 1.3 75.8 - - - +
438C ALA* 1.3 72.1 + - - +
439C SER* 5.6 0.4 - - - -
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LEU* 4.0 0.7 - - + -
66C LEU 3.6 4.7 - - - -
67C LEU* 3.9 12.8 - - + -
436C LEU 4.1 2.0 + - - -
437C VAL* 1.3 84.3 - - - +
439C SER* 1.3 63.7 + - - +
440C GLN 3.2 5.0 + - - +
442C ASN* 3.4 28.7 - - - +
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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