Contacts of the helix formed by residues 622 - 632 (chain f) in PDB entry 5T0J
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 622 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269f GLN* 6.0 3.1 - - + -
273f TYR* 3.2 30.2 - + + -
616f THR* 4.0 23.3 - - + +
620f CYS 3.7 2.0 + - - -
621f PRO* 1.3 69.6 - - - +
623f HIS* 1.3 70.1 + + + +
624f SER 3.1 3.1 - - - -
625f ASP* 3.1 34.1 + - + +
626f ARG* 3.1 48.4 + - + -
629f MET* 3.3 16.8 - - + +
650f ILE* 3.3 13.6 - - + +
653f GLY* 6.1 0.4 - - - -
654f LYS* 3.5 38.1 - - + +
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Residues in contact with HIS 623 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272f LYS* 5.3 14.4 - - - -
621f PRO* 3.3 17.1 - - + -
622f TYR* 1.3 82.7 - + + +
624f SER* 1.3 60.8 + - - +
626f ARG* 3.8 16.5 + - - +
627f GLN* 3.3 37.3 + - + +
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Residues in contact with SER 624 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621f PRO* 3.2 25.2 + - - +
623f HIS* 1.3 79.5 - - - +
625f ASP* 1.3 70.8 + - - +
627f GLN* 3.8 7.6 + - - +
628f LEU* 3.5 21.8 + - - +
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Residues in contact with ASP 625 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607f GLN* 4.9 13.9 + - - +
610f THR* 5.1 10.5 - - - +
611f HIS* 4.6 13.0 + - - -
620f CYS* 6.1 0.2 - - - -
621f PRO 4.9 4.6 - - - +
622f TYR* 3.1 27.0 + - + +
624f SER* 1.3 87.3 + - - +
626f ARG* 1.3 65.2 + - - +
628f LEU* 3.4 5.8 + - - +
629f MET* 3.1 29.4 + - - +
649f ASN* 4.1 18.9 + - - +
653f GLY* 6.2 0.3 - - - -
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Residues in contact with ARG 626 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269f GLN* 5.9 0.6 - - - +
272f LYS* 3.1 34.7 - - - +
273f TYR* 3.3 37.6 - - - +
276f SER* 4.9 6.7 + - - -
622f TYR* 3.1 46.6 + - + +
623f HIS* 3.5 15.5 + - - +
624f SER 3.4 0.2 - - - -
625f ASP* 1.3 78.3 - - - +
627f GLN* 1.3 61.9 + - + +
629f MET* 3.3 15.2 - - + +
630f SER* 2.8 37.7 + - - +
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Residues in contact with GLN 627 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623f HIS* 3.3 23.5 + - + +
624f SER* 4.2 7.0 - - - +
625f ASP 3.3 0.2 - - - -
626f ARG* 1.3 81.1 - - + +
628f LEU* 1.3 60.1 + - - +
630f SER* 4.2 3.9 - - - -
631f GLN* 3.3 39.6 + - - +
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Residues in contact with LEU 628 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586f LEU* 4.8 10.1 - - + -
603f VAL* 5.6 3.1 - - + -
604f ARG* 3.5 24.9 - - - +
607f GLN* 3.4 39.9 - - - +
624f SER 3.5 13.9 + - - +
625f ASP* 3.4 7.5 + - - +
626f ARG 3.3 0.6 - - - -
627f GLN* 1.3 81.1 - - - +
629f MET* 1.3 60.9 + - - +
631f GLN* 4.5 4.3 - - - +
632f VAL* 3.4 24.2 + - + +
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Residues in contact with MET 629 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273f TYR* 3.9 15.9 - - - -
604f ARG* 4.3 5.8 - - - +
622f TYR* 3.3 26.5 - - + +
625f ASP 3.1 26.8 + - - +
626f ARG* 3.3 17.7 - - + +
628f LEU* 1.3 77.8 - - - +
630f SER* 1.3 69.0 + - - +
631f GLN 3.5 0.2 - - - -
632f VAL* 3.8 8.4 - - - +
633f ALA* 3.4 23.2 + - - +
645f LEU* 4.6 2.5 - - - +
646f ASP* 3.8 35.0 - - + +
649f ASN* 3.4 30.1 - - - +
650f ILE* 3.9 4.3 - - + -
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Residues in contact with SER 630 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626f ARG* 2.8 27.6 + - - +
627f GLN* 3.7 5.4 + - - -
628f LEU 3.3 0.4 - - - -
629f MET* 1.3 81.5 - - - +
631f GLN* 1.3 66.7 + - - +
633f ALA* 3.5 9.4 + - - +
634f VAL* 3.2 18.4 - - - +
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Residues in contact with GLN 631 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627f GLN* 3.3 27.3 + - - +
628f LEU* 4.6 4.0 - - - +
629f MET 3.5 0.2 - - - -
630f SER* 1.3 79.2 - - - +
632f VAL* 1.3 60.1 + - - +
633f ALA 3.6 0.2 + - - -
634f VAL* 3.6 18.0 + - - +
635f ALA* 5.2 0.5 + - - +
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Residues in contact with VAL 632 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590f ALA* 3.8 33.2 - - + +
604f ARG* 3.4 24.0 - - - +
628f LEU* 3.4 20.3 + - + +
629f MET 3.8 3.4 - - - +
631f GLN* 1.3 76.5 - - - +
633f ALA* 1.3 60.6 + - - +
634f VAL 3.3 4.5 + - - -
635f ALA* 4.0 14.2 + - + +
642f VAL* 4.8 6.6 - - - +
645f LEU* 3.7 22.4 - - + +
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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