Contacts of the strand formed by residues 628 - 636 (chain A) in PDB entry 4ZGA
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 MET 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A TYR* 3.3 12.5 - - - -
623A SER* 2.8 25.9 + - - -
626A PHE* 3.4 25.8 - - + +
627A LEU* 1.3 79.5 - - - +
629A PRO* 1.3 84.3 - - + +
630A LEU* 4.4 0.6 - - + +
665A GLN* 3.7 13.5 - - - +
700A THR 5.9 0.2 - - - -
703A VAL* 3.9 19.3 - - + -
704A PRO* 3.8 16.8 - - + -
737A PRO* 4.0 14.6 - - + -
739A PHE* 3.9 18.4 - - + -
762A ILE* 4.4 1.8 - - + -
763A PRO* 3.2 29.8 - - + +
765A PRO* 4.2 4.0 - - + -
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Residues in contact with PRO 629 (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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620A SER* 4.3 9.9 - - - +
621A GLY 3.3 8.1 - - - +
622A TYR* 3.7 5.8 - - + -
628A MET* 1.3 93.2 - - + +
630A LEU* 1.3 59.8 + - - +
631A TRP 3.6 10.5 - - - +
632A THR* 3.5 20.9 - - - +
681A LEU* 3.8 21.1 - - + +
700A THR 3.3 26.5 - - - +
701A ASN* 4.7 5.2 - - - +
702A MET 4.9 1.6 - - - +
703A VAL* 4.3 6.5 - - + -
737A PRO* 3.2 25.8 - - - +
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Residues in contact with LEU 630 (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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604A VAL* 4.1 26.7 - - + -
606A TYR* 3.5 27.8 - - + +
608A THR* 5.1 2.9 - - - +
610A TYR* 4.7 13.5 - - + -
621A GLY 2.7 18.2 + - - +
623A SER* 3.5 27.1 - - - +
626A PHE* 4.8 8.3 - - + -
628A MET* 4.4 0.7 - - + +
629A PRO* 1.3 74.4 - - - +
631A TRP* 1.3 68.2 + - + +
737A PRO* 3.2 22.8 - - + +
739A PHE* 6.2 1.8 - - + -
769A TYR* 2.8 18.2 + - - -
834A THR* 5.6 0.2 - - - +
836A LEU* 4.2 17.6 - - + +
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Residues in contact with TRP 631 (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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597A LEU* 4.0 11.9 - - + -
601A ARG* 4.4 4.3 - - + -
602A PRO* 3.6 42.1 + - + +
604A VAL* 5.4 0.2 - - - +
610A TYR* 4.6 10.5 - + - -
612A ILE* 3.5 22.4 - - + -
619A GLU* 3.5 40.6 - - + -
620A SER* 3.1 17.6 - - - -
621A GLY* 2.7 41.2 + - - -
629A PRO* 3.6 3.0 - - - +
630A LEU* 1.3 91.9 - - + +
632A THR* 1.3 70.0 + - - +
633A SER* 3.6 21.1 - - - -
734A ILE* 3.7 11.2 - - + -
735A SER 3.5 7.2 - - - -
769A TYR* 3.3 13.7 - - - +
836A LEU* 4.3 10.8 - - + +
838A PHE* 5.3 0.4 - - + -
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Residues in contact with THR 632 (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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618A PHE* 4.3 8.3 - - + -
619A GLU 3.3 11.0 - - - +
620A SER* 4.0 3.5 - - - -
629A PRO* 3.5 9.2 - - - +
631A TRP* 1.3 77.5 + - - +
633A SER* 1.3 59.1 + - - +
634A TYR* 4.3 8.7 - - + -
681A LEU* 3.1 27.3 - - + +
682A PHE* 3.8 36.3 - - + +
701A ASN* 4.5 2.2 + - - +
733A VAL 3.4 2.4 - - - +
734A ILE* 3.0 5.1 - - - -
735A SER* 2.9 37.4 + - - -
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Residues in contact with SER 633 (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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596A HIS* 2.4 28.1 + - - +
597A LEU* 3.4 24.2 - - - +
618A PHE* 3.6 0.7 - - - +
619A GLU 2.8 35.8 + - - +
631A TRP* 3.6 8.4 - - - -
632A THR* 1.3 73.5 - - - +
634A TYR* 1.3 64.2 + - - +
732A ASN* 3.6 17.7 + - - -
733A VAL 3.2 4.2 + - - -
734A ILE* 3.8 12.6 - - - +
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Residues in contact with TYR 634 (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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596A HIS* 3.8 10.5 - - - -
617A ASP 3.2 21.5 - - - +
618A PHE* 3.8 3.8 - - + -
632A THR* 4.3 13.9 - - + -
633A SER* 1.3 81.2 + - - +
635A THR* 1.3 64.6 + - - +
636A VAL* 3.9 20.0 - - + -
681A LEU 4.3 11.1 + - - -
682A PHE* 3.4 30.3 - + - -
683A PRO* 3.7 20.6 - - + +
686A LEU* 4.3 7.4 - - + -
716A PHE* 5.0 1.6 - - - -
717A GLN* 4.8 5.2 + - - +
721A VAL* 4.4 10.8 - - + +
732A ASN* 4.2 0.2 - - - -
733A VAL* 2.8 77.8 + - + +
735A SER* 4.7 3.6 + - - -
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Residues in contact with THR 635 (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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595A ARG* 2.6 30.5 + - - +
596A HIS* 3.4 18.0 + - - -
598A LEU* 4.1 12.0 - - + +
617A ASP 5.3 0.3 - - - +
634A TYR* 1.3 76.0 - - - +
636A VAL* 1.3 71.9 + - - +
637A SER* 4.4 0.4 + - - -
730A GLY* 5.8 0.4 - - - -
731A VAL 3.3 20.0 - - - +
732A ASN* 2.9 21.1 + - - -
782A ALA* 5.2 4.7 - - + -
783A ASP* 5.1 10.1 - - + +
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Residues in contact with VAL 636 (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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634A TYR* 3.9 20.9 - - + -
635A THR* 1.3 82.2 - - - +
637A SER* 1.3 66.5 + - - +
640A ALA* 4.2 12.1 - - + -
686A LEU* 4.2 14.4 - - + -
721A VAL* 3.7 29.2 - - + -
722A LYS* 4.7 6.7 - - + -
725A ALA* 3.6 22.3 - - + +
730A GLY* 3.0 23.2 - - - -
731A VAL* 3.0 16.9 + - + +
733A VAL* 5.0 0.2 - - + -
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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