Contacts of the strand formed by residues 683 - 688 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A THR* 2.7 21.8 + - - +
651A VAL* 3.6 11.3 - - + +
678A ASP 4.0 1.2 + - - -
679A VAL* 3.4 15.7 - - + -
680A CYS* 3.0 34.1 + - - +
681A GLU 4.4 3.1 - - - +
682A THR* 1.3 77.0 + - - +
684A THR* 1.3 62.6 + - - +
685A HIS 3.5 21.8 - - - +
686A VAL* 3.9 18.4 - - + -
703A ARG* 5.0 1.7 - - - +
705A CYS* 3.2 18.3 - - - -
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Residues in contact with THR 684 (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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648A ARG* 3.6 20.4 - - + +
649A THR 3.1 3.5 + - - -
673A PHE* 3.5 13.2 - - - -
682A THR 3.5 13.7 - - - +
683A THR* 1.3 74.4 - - - +
685A HIS* 1.3 92.8 + - - +
705A CYS* 3.3 10.8 - - - +
706A TRP* 3.0 26.4 + - - +
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Residues in contact with HIS 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ARG* 4.1 11.6 + - - -
649A THR 3.6 1.4 + - - -
650A LEU* 3.3 22.1 - - + +
651A VAL 3.1 22.9 + - - -
673A PHE* 3.6 20.2 - + + -
683A THR* 3.5 5.8 - - - +
684A THR* 1.3 111.3 + - - +
686A VAL* 1.3 63.0 + - - +
687A LEU* 5.4 0.2 - - + -
706A TRP* 3.6 24.7 - + + +
708A LEU* 4.3 3.4 - - + -
712A TRP* 3.7 28.8 - + + -
725A GLU* 3.0 32.7 + - + -
752B ARG* 6.3 0.2 - - - -
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Residues in contact with VAL 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A VAL* 3.6 10.5 - - + +
653A THR* 4.0 22.9 - - + -
679A VAL* 3.5 30.7 - - + -
683A THR* 3.9 6.7 - - + -
685A HIS* 1.3 78.5 - - - +
687A LEU* 1.3 67.4 + - - +
688A SER 4.2 0.4 + - - +
696A ASN 4.1 13.9 - - - +
697A VAL* 4.6 3.1 - - + -
700A GLY* 4.4 11.2 - - - -
705A CYS* 4.5 3.1 - - + -
706A TRP 2.8 15.6 + - - +
707A VAL* 3.4 18.4 - - + -
708A LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 687 (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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650A LEU* 3.5 35.7 - - + -
651A VAL 2.9 13.1 + - - +
652A MET* 3.5 5.3 - - + -
653A THR* 2.9 28.3 + - - +
655A MET* 3.6 14.0 - - + +
663A VAL* 4.2 12.3 - - + -
685A HIS* 5.4 0.2 - - + -
686A VAL* 1.3 79.7 - - - +
688A SER* 1.3 60.0 + - - +
708A LEU* 3.7 20.6 - - + +
709A SER 4.3 7.4 - - - +
710A TYR* 5.4 3.4 - - + -
712A TRP* 3.7 26.2 - - + -
713A VAL* 3.6 28.3 - - + -
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A THR* 3.3 19.5 - - - -
654A SER* 5.0 0.4 - - - -
655A MET* 3.7 3.8 - - - +
686A VAL* 4.2 0.8 + - - +
687A LEU* 1.3 74.1 - - - +
689A GLY* 1.3 61.3 + - - +
690A LYS 4.3 7.9 - - - -
691A PRO* 4.2 13.8 - - - +
692A LEU 5.2 0.7 - - - -
697A VAL* 4.9 7.9 - - - -
707A VAL* 5.5 2.2 - - - +
708A LEU 3.2 8.2 + - - -
709A SER* 4.1 1.9 - - - -
710A TYR 3.4 22.9 + - - -
730A LEU* 3.1 31.9 - - - +
734A PHE* 6.1 0.2 - - - -
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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