Contacts of the helix formed by residues 710 - 718 (chain B) in PDB entry 3T6A
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 LEU 710 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564B ALA* 4.7 6.3 - - + -
583B LEU* 3.8 10.8 - - + -
586B ILE* 3.7 26.9 - - + -
598B ILE* 4.2 25.8 - - + -
645B TYR* 4.0 19.5 - - + -
696B GLU* 4.8 1.4 + - - -
707B VAL* 3.9 18.6 - - + -
708B PRO* 3.4 40.2 - - + +
709B LEU* 1.3 73.4 - - - +
711B MET* 1.3 56.7 + - - +
712B PRO* 3.6 2.4 - - - +
713B LEU* 3.6 11.0 + - - +
714B VAL* 2.9 37.4 + - + +
750B MET* 4.0 6.3 - - + -
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Residues in contact with MET 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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598B ILE* 4.3 5.6 - - - +
599B ILE* 4.0 40.8 - - + +
602B HIS* 3.6 56.1 - - + +
603B ASN* 4.3 3.6 - - - +
645B TYR* 4.6 3.8 - - + -
648B SER* 4.8 2.7 - - - +
709B LEU* 2.8 14.0 + - + +
710B LEU* 1.3 73.4 - - - +
712B PRO* 1.3 67.7 - - + +
714B VAL* 3.8 2.3 - - - +
715B THR* 2.9 33.9 + - - -
723B THR* 4.0 19.1 - - + -
728B ASP* 3.8 18.6 - - + +
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Residues in contact with PRO 712 (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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692B HIS* 4.7 11.0 - - + +
709B LEU* 3.5 32.3 - - + -
710B LEU 3.8 0.7 - - - +
711B MET* 1.3 96.5 - - + +
713B LEU* 1.3 58.3 + - - +
715B THR* 2.8 26.4 - - + +
716B LEU* 3.0 8.8 + - - +
728B ASP* 3.4 18.6 - - - +
730B TRP* 3.2 20.8 - - + -
743B HIS* 3.6 26.7 - - + +
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Residues in contact with LEU 713 (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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737A CYS* 3.9 11.0 - - - -
586B ILE* 4.7 10.5 - - + -
587B THR* 4.9 1.6 - - + -
710B LEU* 3.8 12.3 - - - +
712B PRO* 1.3 77.9 - - - +
714B VAL* 1.3 65.9 + - + +
716B LEU* 3.1 8.3 + - + +
717B MET* 3.1 30.9 + - + +
743B HIS* 4.3 22.6 + - + +
744B LEU* 3.8 29.2 - - + -
747B ALA* 3.6 30.3 - - + -
750B MET* 3.9 21.5 - - + -
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Residues in contact with VAL 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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586B ILE* 4.3 20.9 - - + +
595B ARG* 3.6 39.7 - - + +
598B ILE* 4.4 14.8 - - + -
599B ILE* 3.2 35.9 - - + -
710B LEU* 2.9 23.5 + - + +
711B MET* 3.9 4.0 - - - +
713B LEU* 1.3 80.6 - - + +
715B THR* 1.3 57.3 + - - +
717B MET* 3.8 1.3 + - - +
718B GLU* 3.2 28.4 + - - +
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Residues in contact with THR 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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719A ARG* 3.1 21.7 + - - -
599B ILE* 4.7 6.3 - - - -
711B MET* 2.9 18.6 + - - +
712B PRO* 2.8 19.7 - - + +
714B VAL* 1.3 77.8 - - - +
716B LEU* 1.3 62.0 + - - +
718B GLU 3.0 23.3 - - - +
721B ALA* 4.1 5.0 - - - +
723B THR* 4.4 5.8 - - - +
728B ASP* 3.0 28.0 + - + +
729B MET* 3.8 7.1 - - - +
730B TRP* 2.8 35.2 - - - +
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Residues in contact with LEU 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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716A LEU* 4.2 30.0 - - + +
719A ARG* 4.6 3.2 + - - +
740A MET* 5.2 1.8 - - - -
744A LEU* 4.8 0.4 - - + -
712B PRO 3.0 18.8 + - - +
713B LEU* 3.4 6.5 - - - +
715B THR* 1.3 79.6 - - - +
717B MET* 1.3 59.7 + - + +
719B ARG* 4.2 14.7 - - - +
730B TRP* 3.7 30.7 - - + +
740B MET* 3.7 45.3 - - + +
743B HIS* 5.0 5.2 - - + -
744B LEU* 4.1 33.2 - - + -
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Residues in contact with MET 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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716A LEU* 5.8 0.4 - - - -
730A TRP* 4.4 5.5 - - - +
735A GLN* 3.6 50.7 + - + +
737A CYS* 3.5 23.8 - - - -
740A MET* 3.4 31.8 - - + +
586B ILE 3.5 14.8 - - - +
587B THR 4.0 4.5 - - - +
595B ARG* 3.5 35.9 - - - +
713B LEU* 3.1 26.8 + - + +
714B VAL* 4.1 4.5 - - - +
716B LEU* 1.3 76.8 - - + +
718B GLU* 1.3 59.5 + - - +
719B ARG* 3.6 5.9 + - - +
744B LEU* 5.1 0.2 - - + -
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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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719A ARG* 2.6 28.1 + - - -
735A GLN* 3.2 20.3 + - - +
592B HIS* 3.0 32.5 + - - -
595B ARG* 2.6 41.2 + - + +
596B LEU* 4.2 10.4 - - + +
599B ILE* 4.2 7.4 - - + -
714B VAL 3.2 20.9 + - - +
715B THR 3.0 4.1 + - - +
716B LEU 3.3 0.4 - - - -
717B MET* 1.3 77.9 - - - +
719B ARG* 1.3 50.0 + - - +
720B GLN* 3.0 9.9 + - - +
721B ALA* 3.1 22.7 + - + +
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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