Contacts of the strand formed by residues 385 - 389 (chain A) in PDB entry 1MAQ
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 GLY 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A PHE* 4.6 2.0 - - - -
363A THR* 2.7 46.3 + - - +
364A GLY 4.9 0.9 - - - -
365A LEU* 4.1 14.5 + - - -
370A VAL* 4.5 9.2 - - - -
381A MET* 5.1 2.2 - - - -
382A THR 3.2 6.0 + - - -
383A LYS 3.2 5.5 + - - -
384A ASP* 1.3 79.7 - - - +
386A ARG* 1.3 59.3 + - - +
387A ILE* 4.2 2.5 - - - +
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Residues in contact with ARG 386 (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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17A ILE* 3.5 27.0 - - - +
35A LEU 4.2 1.7 - - - +
36A GLY 3.5 19.8 + - - +
140A TRP* 4.6 0.8 - - - -
194A ASN* 2.6 27.6 + - - +
195A PRO* 3.3 27.3 - - + +
360A PHE* 3.4 30.2 - - + -
361A CYS 3.4 10.3 - - - +
362A PHE* 4.0 10.3 - - + -
381A MET* 3.4 17.3 - - - +
382A THR* 3.3 21.5 + - - +
384A ASP* 3.1 20.2 + - - +
385A GLY* 1.3 78.1 - - - +
387A ILE* 1.3 61.7 + - - +
412A PGU 2.5 41.6 + - - -
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Residues in contact with ILE 387 (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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35A LEU* 3.7 20.9 - - + -
36A GLY 5.3 0.2 - - - -
337A LEU* 4.6 8.3 - - + -
360A PHE* 3.2 10.6 - - - +
361A CYS* 2.9 43.2 + - + +
363A THR* 3.9 22.4 - - + -
365A LEU* 5.6 0.7 - - + -
379A ILE* 6.0 0.2 - - + -
381A MET* 3.4 34.5 - - + -
385A GLY 4.2 0.2 - - - +
386A ARG* 1.3 73.3 - - - +
388A SER* 1.3 60.3 + - - +
389A VAL* 3.5 19.4 + - + +
400A LEU* 4.1 26.2 - - + -
404A ILE* 4.8 10.1 - - + -
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Residues in contact with SER 388 (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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34A ASN 5.0 1.3 - - - -
35A LEU* 3.0 39.2 + - - +
36A GLY 4.0 3.1 - - - -
37A VAL 3.5 25.5 + - - -
38A GLY* 4.0 6.6 - - - -
39A ALA 4.3 3.3 + - - -
359A MET 3.8 5.3 + - - -
360A PHE* 4.0 7.6 - - - -
387A ILE* 1.3 73.4 - - - +
389A VAL* 1.3 62.5 + - - +
390A ALA* 3.8 10.7 + - - +
391A GLY* 3.2 17.9 + - - -
392A VAL* 3.7 0.9 - - - +
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Residues in contact with VAL 389 (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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330A ILE* 3.3 34.3 - - + +
333A MET* 4.1 8.9 - - + +
334A ARG* 3.7 37.2 - - + +
337A LEU* 4.5 21.5 - - + -
353A ILE* 5.3 1.3 - - + -
359A MET 3.1 8.4 + - - +
360A PHE 4.7 2.0 - - - -
361A CYS* 4.4 19.7 - - + -
387A ILE* 3.5 9.1 + - + -
388A SER* 1.3 70.0 - - - +
390A ALA* 1.3 63.8 + - - +
392A VAL* 3.1 30.1 + - + +
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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