Contacts of the helix formed by residues 710 - 719 (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 TYR 710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B MET* 4.2 24.7 - - + -
659B LYS* 3.8 57.0 - - + +
662B VAL* 3.1 34.6 - - + +
663B VAL* 4.0 16.6 - - + -
687B LEU* 5.4 4.2 - - + +
688B SER 4.4 5.5 + - - +
689B GLY* 5.2 4.9 - - - -
708B LEU 4.3 0.2 + - - -
709B SER* 1.3 72.2 - - - +
711B ASP* 1.3 63.9 + - - +
712B TRP 3.4 0.2 - - - -
713B VAL* 3.3 21.3 + - + +
714B LEU* 3.3 44.0 + - + +
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Residues in contact with ASP 711 (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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709B SER* 2.8 13.2 + - - +
710B TYR* 1.3 79.6 + - - +
712B TRP* 1.3 66.3 + - - +
713B VAL 2.9 2.5 - - - -
714B LEU* 2.8 29.5 + - - +
715B TRP* 2.9 25.0 + - + +
728B PHE* 3.4 27.6 - - + -
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Residues in contact with TRP 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B LEU* 4.6 11.9 - - + -
673B PHE* 4.1 8.3 - + - -
685B HIS* 3.2 37.0 - + - -
687B LEU* 4.2 11.2 - - + -
708B LEU* 4.0 17.3 - - + -
709B SER 3.1 12.7 + - - +
711B ASP* 1.3 78.3 - - - +
713B VAL* 1.3 59.8 + - + +
716B SER* 2.5 41.2 + - - -
722B TRP* 3.4 46.7 - + + -
723B ILE* 3.0 31.6 + - + +
724B SER 3.2 19.5 + - - -
725B GLU* 3.6 21.7 - - + +
728B PHE* 3.6 29.1 - + + -
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B LEU* 6.2 0.2 - - + -
662B VAL* 4.6 6.1 - - + -
663B VAL* 4.0 29.4 - - + -
666B VAL* 4.2 20.0 - - + +
687B LEU* 4.0 18.8 - - + -
709B SER 4.4 0.2 + - - -
710B TYR* 3.3 32.8 + - + +
711B ASP 2.9 0.6 - - - -
712B TRP* 1.3 84.0 - - + +
714B LEU* 1.3 70.2 + - - +
716B SER* 3.3 5.9 + - - -
717B LEU* 3.0 21.7 + - + +
722B TRP* 4.3 17.9 - - + -
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Residues in contact with LEU 714 (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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662B VAL* 5.0 5.2 - - + -
710B TYR* 3.3 52.2 + - + +
711B ASP* 2.8 25.6 + - - +
713B VAL* 1.3 78.9 - - + +
715B TRP* 1.3 60.5 + - + +
717B LEU* 3.1 12.9 + - + +
718B GLU* 3.0 24.8 + - - +
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Residues in contact with TRP 715 (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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711B ASP* 2.9 25.4 + - + +
714B LEU* 1.3 77.2 - - + +
716B SER* 1.3 65.6 + - - +
717B LEU 3.0 1.8 - - - -
718B GLU* 4.2 27.1 - - + -
719B LEU* 3.1 47.8 + - + +
723B ILE* 3.4 22.4 - - + -
728B PHE* 4.0 21.2 - + - -
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Residues in contact with SER 716 (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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670B LEU* 3.3 7.2 - - - +
712B TRP* 2.5 27.4 + - - -
713B VAL 3.5 6.1 - - - -
715B TRP* 1.3 77.0 - - - +
717B LEU* 1.3 56.6 + - - +
720B GLY 3.2 2.1 + - - -
721B HIS 2.9 40.0 + - - +
722B TRP* 3.5 30.3 - - - -
723B ILE* 3.2 24.9 + - - +
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Residues in contact with LEU 717 (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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662B VAL* 5.1 8.1 - - + -
665B GLN* 6.1 1.1 - - + +
666B VAL* 3.8 23.3 - - + -
669B LYS* 2.9 31.6 - - - +
670B LEU* 4.6 11.7 - - + -
713B VAL 3.0 11.9 + - - +
714B LEU* 3.3 14.4 - - + +
715B TRP 3.0 0.6 - - - -
716B SER* 1.3 75.7 - - - +
718B GLU* 1.3 68.4 + - - +
719B LEU 3.0 1.6 - - - -
720B GLY* 3.0 13.1 + - - -
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Residues in contact with GLU 718 (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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714B LEU 3.0 13.1 + - - +
715B TRP* 3.3 34.2 + - + +
717B LEU* 1.3 77.7 - - - +
719B LEU* 1.3 65.7 + - + +
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Residues in contact with LEU 719 (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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715B TRP* 3.1 32.4 + - + +
716B SER 4.5 0.9 - - - +
717B LEU 3.0 0.4 - - - -
718B GLU* 1.3 89.1 - - + +
720B GLY* 1.3 63.1 + - - +
721B HIS* 3.3 26.6 + - + +
723B ILE* 3.3 32.3 - - + -
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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