Contacts of the helix formed by residues 652 - 661 (chain A) in PDB entry 4IQJ
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 ASP 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A PRO* 4.2 14.0 + - + +
651A ASP* 1.3 75.6 + - - +
653A PRO* 1.3 79.2 - - - +
654A LYS* 3.6 12.9 + - - +
655A THR* 3.0 33.1 + - - +
656A PHE* 3.3 19.2 + - - -
826A TYR* 3.2 19.3 + - - +
830A TYR* 3.7 21.2 - - + -
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Residues in contact with PRO 653 (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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651A ASP 3.5 7.6 - - - +
652A ASP* 1.3 93.7 - - - +
654A LYS* 1.3 71.2 + - + +
655A THR 3.1 0.5 + - - -
656A PHE* 3.1 7.0 + - + +
657A GLU* 3.0 39.1 + - + +
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Residues in contact with LYS 654 (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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652A ASP* 3.5 12.9 + - - +
653A PRO* 1.3 83.5 - - + +
655A THR* 1.3 62.0 + - - +
657A GLU* 3.6 20.3 + - - +
658A LEU* 3.2 22.5 + - - +
661A ARG* 4.5 4.1 + - - +
833A ALA* 5.0 14.8 - - - -
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Residues in contact with THR 655 (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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652A ASP* 3.0 24.7 + - - +
653A PRO 3.1 0.8 + - - -
654A LYS* 1.3 76.8 - - - +
656A PHE* 1.3 63.4 + - - +
658A LEU* 3.4 7.5 + - - +
659A LEU* 3.2 25.0 + - + +
826A TYR* 3.6 30.0 + - + +
829A ALA* 3.7 28.5 - - + -
830A TYR* 3.4 30.1 + - - +
833A ALA* 5.5 2.0 - - - +
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Residues in contact with PHE 656 (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 3.7 17.3 - - - -
651A ASP* 4.2 6.5 - - - -
652A ASP 3.3 21.1 - - - -
653A PRO* 3.1 8.5 + - + +
655A THR* 1.3 78.1 - - - +
657A GLU* 1.3 56.4 + - + +
659A LEU* 3.4 14.6 + - + +
660A SER* 2.6 38.0 + - - -
684A PRO* 3.3 25.1 - - + +
685A ARG* 3.3 25.1 - - - +
686A ARG* 3.2 36.3 - - - -
687A LEU* 3.4 6.5 - - - -
690A ILE* 4.2 17.0 - - + -
826A TYR* 3.8 24.0 - + - -
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Residues in contact with GLU 657 (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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653A PRO* 3.0 32.1 + - - +
654A LYS* 3.8 25.3 + - - +
656A PHE* 1.3 75.8 - - + +
658A LEU* 1.3 63.0 + - - +
660A SER* 3.7 7.6 - - - -
661A ARG* 3.2 42.6 + - - +
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Residues in contact with LEU 658 (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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654A LYS 3.2 13.5 + - - +
655A THR* 3.5 11.2 - - - +
656A PHE 3.2 0.2 - - - -
657A GLU* 1.3 75.1 - - - +
659A LEU* 1.3 76.8 + - + +
661A ARG* 3.4 20.1 + - - +
663A GLU* 3.3 61.4 + - - +
667A VAL* 4.7 1.3 - - + -
829A ALA* 4.2 11.0 - - + +
832A LYS* 3.7 22.2 - - + +
833A ALA* 3.5 34.1 - - - +
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Residues in contact with LEU 659 (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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655A THR* 3.2 18.0 + - + +
656A PHE* 3.8 19.3 - - + +
658A LEU* 1.3 78.4 - - + +
660A SER* 1.3 65.6 + - - +
662A GLY* 3.1 11.8 + - - -
664A THR* 3.8 26.2 - - + -
667A VAL* 4.3 8.7 - - + -
670A LEU* 4.5 10.5 - - + -
679A VAL* 3.1 31.2 - - + +
684A PRO* 4.0 5.8 - - + -
690A ILE* 3.4 34.5 - - + -
825A SER 5.7 0.2 - - - +
826A TYR* 5.6 0.7 - - + -
829A ALA* 4.0 24.7 - - + -
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Residues in contact with SER 660 (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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656A PHE 2.6 26.1 + - - -
657A GLU* 3.7 10.6 - - - -
658A LEU 3.3 0.2 - - - -
659A LEU* 1.3 76.8 - - - +
661A ARG* 1.3 56.9 + - - +
662A GLY 3.3 1.3 + - - -
679A VAL 4.3 2.5 - - - -
680A ARG* 3.5 8.7 - - - -
683A LYS* 2.8 51.2 + - - +
684A PRO* 3.5 24.7 + - - +
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Residues in contact with ARG 661 (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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654A LYS* 4.5 4.2 + - - +
657A GLU* 3.2 45.0 + - - +
658A LEU* 3.4 14.9 + - - +
659A LEU 3.2 0.8 - - - -
660A SER* 1.3 75.7 - - - +
662A GLY* 1.3 59.6 + - - +
663A GLU* 3.1 48.9 + - - +
680A ARG* 2.9 25.6 + - - +
683A LYS* 5.0 2.0 - - - +
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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