Contacts of the strand formed by residues 683 - 688 (chain B) in PDB entry 3T1N
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 683 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B THR* 2.9 15.8 + - - +
651B VAL* 3.3 33.3 - - + +
678B ASP 3.8 1.9 + - - -
679B VAL* 3.4 12.7 - - + -
680B CYS* 3.1 30.8 + - - +
681B GLU 4.5 3.3 - - - +
682B THR* 1.3 76.9 - - - +
684B THR* 1.3 63.3 + - - +
685B HIS 3.4 16.8 - - - +
686B VAL* 4.1 12.3 - - + -
703B ARG* 5.2 1.7 - - - +
705B CYS* 3.4 14.7 - - - -
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Residues in contact with THR 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ARG* 3.8 25.9 + - + +
649B THR 3.3 4.3 + - - -
673B PHE* 3.7 12.0 - - - -
682B THR 3.4 8.2 + - - +
683B THR* 1.3 78.8 - - - +
685B HIS* 1.3 83.0 + - - +
705B CYS* 3.2 10.2 - - - +
706B TRP* 3.0 29.9 + - - +
745B HIS* 5.8 0.7 + - - -
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Residues in contact with HIS 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ARG* 3.8 17.3 - - - -
649B THR 3.6 1.8 + - - +
650B LEU* 3.1 23.0 - - + -
651B VAL 3.0 23.9 + - - -
673B PHE* 3.3 22.1 - + + -
683B THR* 3.4 8.5 - - - +
684B THR* 1.3 101.9 + - - +
686B VAL* 1.3 63.1 + - - +
687B LEU* 5.6 0.4 - - + -
706B TRP* 3.6 20.9 - + - -
708B LEU* 4.0 15.9 - - + -
712B TRP* 3.2 34.2 - + - -
725B GLU* 3.3 21.7 + - - +
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Residues in contact with VAL 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B VAL* 3.4 14.8 - - + +
653B THR* 4.6 12.8 - - + -
679B VAL* 4.3 14.1 - - + -
683B THR* 4.1 14.6 - - + -
685B HIS* 1.3 80.1 - - - +
687B LEU* 1.3 79.2 + - - +
688B SER* 5.8 0.2 - - - -
696B ASN* 4.9 9.9 - - + +
697B VAL* 4.9 5.4 - - - -
700B GLY* 4.5 8.5 - - - -
705B CYS* 4.1 14.1 - - + -
706B TRP 2.8 16.4 + - - +
707B VAL* 4.5 15.3 - - + -
708B LEU* 2.9 24.8 + - - +
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Residues in contact with LEU 687 (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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650B LEU* 3.6 35.0 - - + -
651B VAL 2.9 11.2 + - - +
652B MET* 3.5 3.8 - - + -
653B THR* 2.8 32.3 + - - +
655B MET* 3.6 15.7 - - + +
663B VAL* 4.2 11.0 - - + -
686B VAL* 1.3 83.7 - - - +
688B SER* 1.3 61.1 + - - +
708B LEU* 3.4 22.9 - - + +
709B SER 4.1 14.1 - - - +
710B TYR* 5.6 2.0 - - - -
712B TRP* 4.2 17.3 - - + -
713B VAL* 4.0 24.7 - - + -
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Residues in contact with SER 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B THR* 3.3 19.9 + - - +
654B SER* 4.3 0.2 + - - -
655B MET* 4.4 1.6 - - - -
686B VAL* 5.8 0.2 - - - -
687B LEU* 1.3 72.5 - - - +
689B GLY* 1.3 62.4 + - - +
690B LYS* 2.7 34.5 + - - -
691B PRO* 3.6 5.0 - - - +
692B LEU 3.9 3.8 + - - -
697B VAL* 4.8 6.7 - - - -
707B VAL* 5.4 2.7 - - - +
708B LEU 3.0 14.5 + - - +
709B SER* 4.3 9.9 - - - -
710B TYR 4.4 2.7 + - - -
730B LEU* 3.7 25.5 - - - +
734B PHE* 5.3 0.9 - - - -
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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