Contacts of the helix formed by residues 710 - 718 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A ALA* 4.7 6.7 - - + -
583A LEU* 4.1 11.2 - - + -
586A ILE* 3.5 29.8 - - + -
598A ILE* 4.3 28.0 - - + -
645A TYR* 4.3 15.3 - - + -
696A GLU* 4.9 1.6 + - - -
707A VAL* 4.1 17.3 - - + -
708A PRO* 3.3 35.4 - - + +
709A LEU* 1.3 76.4 - - - +
711A MET* 1.3 63.8 + - - +
712A PRO* 3.5 2.9 - - - +
713A LEU* 3.2 13.7 + - + +
714A VAL* 2.9 26.2 + - + +
750A MET* 3.9 8.7 - - + -
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Residues in contact with MET 711 (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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598A ILE* 4.2 11.0 - - - +
599A ILE* 3.6 48.9 - - + +
602A HIS* 3.8 51.6 - - + +
603A ASN* 4.7 3.1 - - - +
645A TYR* 4.5 0.7 - - - -
648A SER* 5.0 1.3 - - - +
709A LEU* 2.6 17.2 + - + +
710A LEU* 1.3 72.6 - - - +
712A PRO* 1.3 69.7 - - + +
714A VAL* 3.9 2.7 - - - +
715A THR* 3.1 28.6 + - - +
723A THR* 4.6 15.5 - - + -
728A ASP* 4.5 14.8 - - + +
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Residues in contact with PRO 712 (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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692A HIS* 4.4 10.1 - - + +
709A LEU* 3.6 32.5 - - + -
710A LEU 3.7 1.8 - - - +
711A MET* 1.3 97.4 - - + +
713A LEU* 1.3 56.2 + - - +
715A THR* 4.4 2.0 - - - -
716A LEU* 3.2 10.7 + - - +
728A ASP* 3.4 23.8 - - - +
730A TRP* 3.2 42.0 + - + +
743A HIS* 3.7 22.9 - - + +
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Residues in contact with LEU 713 (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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586A ILE* 4.3 13.7 - - + -
587A THR* 5.0 0.9 - - + -
710A LEU* 3.2 13.1 + - + +
712A PRO* 1.3 76.2 - - - +
714A VAL* 1.3 66.7 + - + +
715A THR 3.1 2.2 + - - -
716A LEU* 3.4 6.2 + - + +
717A MET* 3.1 36.3 + - + +
743A HIS* 4.2 21.5 + - + +
744A LEU* 3.5 26.2 - - + -
747A ALA* 3.3 35.7 - - + -
750A MET* 4.1 20.0 - - + -
737B CYS* 3.8 10.8 - - - -
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Residues in contact with VAL 714 (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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586A ILE* 4.3 21.1 - - + -
595A ARG* 3.5 38.4 - - + +
598A ILE* 4.2 19.7 - - + -
599A ILE* 3.3 35.4 - - + -
710A LEU* 2.9 22.1 + - + +
711A MET* 3.9 4.9 - - - +
713A LEU* 1.3 79.3 - - + +
715A THR* 1.3 56.4 + - - +
717A MET* 3.8 1.4 + - - +
718A GLU* 3.1 28.1 + - - +
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Residues in contact with THR 715 (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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599A ILE* 4.7 5.0 - - - +
711A MET* 3.1 19.6 + - - +
712A PRO* 3.8 1.3 - - - +
713A LEU 3.1 0.6 - - - -
714A VAL* 1.3 77.3 - - - +
716A LEU* 1.3 63.2 + - - +
717A MET 3.2 1.6 - - - -
718A GLU* 3.0 24.1 + - - +
721A ALA* 4.2 7.3 - - - +
723A THR* 4.2 12.3 - - - +
728A ASP* 2.8 34.5 + - + +
729A MET* 4.1 10.1 - - + +
730A TRP* 2.9 26.7 - - + +
719B ARG* 3.1 14.6 + - - +
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Residues in contact with LEU 716 (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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712A PRO 3.2 14.2 + - - +
713A LEU* 3.6 8.7 - - - +
715A THR* 1.3 82.0 - - - +
717A MET* 1.3 60.0 + - + +
719A ARG* 4.0 15.1 - - - +
730A TRP* 3.9 34.8 - - + +
740A MET* 4.0 36.6 - - + +
743A HIS* 5.6 2.5 - - + -
744A LEU* 4.4 26.9 - - + -
716B LEU* 4.2 35.3 - - + +
717B MET* 5.8 0.2 - - - -
719B ARG* 4.5 6.5 + - - +
730B TRP* 6.0 0.3 - - - +
740B MET* 5.0 3.1 - - - -
744B LEU* 4.7 2.2 - - + -
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Residues in contact with MET 717 (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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586A ILE 3.5 26.5 - - - +
587A THR 4.2 1.3 - - - +
595A ARG* 3.6 26.9 - - - +
713A LEU* 3.1 30.0 + - + +
714A VAL 3.8 5.4 - - - +
716A LEU* 1.3 77.7 - - + +
718A GLU* 1.3 58.0 + - - +
719A ARG* 3.6 5.6 + - - +
744A LEU* 5.2 0.2 - - + -
730B TRP* 3.9 7.8 - - - +
735B GLN* 3.3 41.0 + - + +
737B CYS* 3.5 23.3 - - - +
740B MET* 3.4 39.3 - - + -
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Residues in contact with GLU 718 (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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592A HIS* 2.8 42.1 + - - -
595A ARG* 2.6 42.7 + - + +
596A LEU* 4.2 7.6 - - + +
599A ILE* 4.2 7.4 - - + -
714A VAL 3.1 21.6 + - - +
715A THR 3.0 5.7 + - - +
717A MET* 1.3 76.6 - - - +
719A ARG* 1.3 55.3 + - - +
720A GLN* 3.0 7.7 + - - +
721A ALA* 2.9 26.0 + - + +
719B ARG* 2.9 18.5 + - - -
735B GLN* 3.1 15.9 + - - +
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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