Contacts of the strand formed by residues 521 - 528 (chain B) in PDB entry 3SRH
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 THR 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B THR* 3.3 23.1 + - - +
411B THR* 3.3 18.7 + - + -
429B VAL* 5.0 0.7 - - + -
430B LEU 4.4 7.9 + - - +
436B SER* 2.5 33.0 + - - +
511B LEU* 4.1 32.5 - - + +
512B THR* 3.6 19.4 - - - +
513B GLY* 4.3 2.0 + - - -
518B SER 4.4 5.5 + - - -
519B GLY 2.7 10.9 + - - -
520B PHE* 1.3 71.1 - - - +
522B ASN* 1.3 61.5 + - - +
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Residues in contact with ASN 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET 3.4 6.1 - - - +
525A ARG* 4.4 4.2 - - - +
526A VAL* 3.3 45.1 + - + +
527A VAL* 4.0 16.0 - - - +
407B PRO* 5.2 4.3 - - + -
411B THR* 3.4 21.4 + - - +
512B THR 3.4 1.6 + - - -
513B GLY 3.5 7.1 - - - -
514B TRP* 3.2 41.6 - - + +
520B PHE* 4.6 1.8 - - + +
521B THR* 1.3 73.7 - - - +
523B THR* 1.3 79.7 + - - +
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A THR* 5.1 6.3 - - + -
524A MET 3.4 5.2 - - - -
525A ARG* 3.6 32.1 - - + -
510B VAL 3.4 3.6 - - - +
511B LEU* 3.4 6.6 - - - +
512B THR* 2.5 51.1 + - - +
513B GLY 3.6 11.4 - - - +
514B TRP* 4.7 3.1 - - + +
521B THR* 5.0 0.2 - - - +
522B ASN* 1.3 93.2 + - - +
524B MET* 1.3 60.6 + - - +
525B ARG* 5.0 6.3 - - - -
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Residues in contact with MET 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 4.1 26.5 - - + +
414A GLY* 4.8 1.6 - - - -
522A ASN 3.7 0.7 - - - +
523A THR* 3.5 3.6 - - - +
524A MET* 2.8 64.3 + - + +
411B THR* 4.4 0.7 - - + -
414B GLY 4.0 6.1 - - - +
415B ALA* 3.7 26.7 - - + -
418B ALA* 4.0 11.0 - - + -
509B ILE* 3.7 19.7 - - + -
510B VAL 3.4 2.9 - - - -
511B LEU* 3.8 14.4 - - + -
522B ASN 3.7 1.0 + - - -
523B THR* 1.3 73.8 - - - +
525B ARG* 1.3 63.3 + - - +
526B VAL* 3.8 26.9 - - + -
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Residues in contact with ARG 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A TRP* 6.4 0.2 - - - +
522A ASN* 3.2 6.4 - - - +
523A THR* 3.7 31.0 - - + +
485B VAL* 4.2 22.0 - - - +
486B ASP* 4.6 12.1 + - - -
489B VAL* 5.2 9.5 - - - +
508B VAL 3.6 0.9 - - - +
509B ILE* 3.4 7.3 - - - +
510B VAL* 2.8 61.6 + - + +
512B THR* 4.3 9.6 + - - -
523B THR* 5.0 10.5 - - - -
524B MET* 1.3 80.7 - - - +
526B VAL* 1.3 63.9 + - - +
527B VAL* 3.9 25.1 + - + +
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO* 3.6 30.1 - - + +
410A ALA* 4.4 10.3 - - + -
411A THR* 3.3 31.4 - - - +
522A ASN* 3.0 28.2 + - + +
422B CYS* 4.7 0.7 - - - -
507B VAL* 3.5 27.4 - - + -
508B VAL 3.6 4.5 - - - +
509B ILE* 4.2 15.3 - - + -
524B MET* 3.8 18.2 - - + -
525B ARG* 1.3 73.8 - - - +
527B VAL* 1.3 58.5 + - - +
528B PRO* 4.5 1.9 - - - +
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO* 6.4 0.2 - - - -
522A ASN* 3.7 15.5 - - - +
489B VAL* 5.6 2.7 - - + -
493B MET* 5.2 4.5 - - - -
507B VAL* 4.4 4.3 - - - -
508B VAL* 2.9 38.9 + - + +
510B VAL* 3.6 31.2 - - + -
525B ARG* 4.4 26.5 - - + +
526B VAL* 1.3 79.7 - - - +
528B PRO* 1.3 73.7 - - + +
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Residues in contact with PRO 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO* 6.3 2.9 - - + -
493B MET* 4.7 0.7 - - - +
505B GLY* 4.4 11.9 - - - +
506B ASP 3.2 10.5 - - - +
507B VAL* 4.4 3.6 - - + -
508B VAL* 4.9 0.2 - - - -
526B VAL 4.5 1.8 - - - +
527B VAL* 1.3 97.8 - - + +
529B VAL* 1.3 66.5 + - - +
530B PRO* 3.4 10.7 - - - +
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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