Contacts of the strand formed by residues 620 - 627 (chain A) in PDB entry 4Z96
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 ILE 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A VAL* 4.5 11.2 - - + +
609A LEU* 3.6 30.7 - - + -
610A SER* 4.4 22.0 - - - -
613A MET* 6.5 0.4 - - + -
615A PHE* 3.5 32.3 - - + -
616A PRO 3.9 1.1 - - - +
617A GLN* 3.4 23.7 - - + +
618A ASP 5.0 0.5 - - - -
619A GLN* 1.3 85.2 + - - +
621A ARG* 1.3 66.0 + - - +
622A LEU* 4.9 5.8 - - + -
640A ASN* 4.2 6.2 + - - +
662A LEU* 3.6 13.7 - - + -
663A GLU 3.2 11.7 - - - +
664A THR* 4.1 3.1 - - - +
676A LEU* 3.8 6.5 - - - +
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Residues in contact with ARG 621 (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 ILE* 1.3 79.0 + - - +
622A LEU* 1.3 72.3 + - - +
623A TRP* 3.4 31.2 - - + +
637A MET* 5.3 6.3 - - - -
638A LEU 4.8 5.8 - - - -
640A ASN* 3.7 18.2 - - - +
662A LEU* 3.8 1.4 - - - -
663A GLU* 2.9 34.9 + - - +
676A LEU* 3.7 23.7 + - + +
677A PRO 2.9 27.3 + - - -
678A LYS* 4.9 0.2 - - - +
679A PHE* 3.8 14.1 - - - +
706A TYR* 3.1 26.7 + - - -
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Residues in contact with LEU 622 (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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569A ILE* 4.7 3.4 - - + -
602A LEU* 5.1 4.3 - - + -
605A PHE* 4.0 27.1 - - + -
606A VAL* 3.6 28.5 - - + -
609A LEU* 4.4 9.2 - - + -
620A ILE* 4.9 9.2 - - + -
621A ARG* 1.3 81.8 - - - +
623A TRP* 1.3 63.5 + - - +
624A PRO* 3.5 7.9 - - - +
638A LEU* 3.7 27.4 + - + +
640A ASN* 3.3 27.0 - - - +
660A ILE* 3.5 27.4 - - + -
661A PHE 3.5 4.0 - - - -
662A LEU* 4.7 10.3 - - + -
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Residues in contact with TRP 623 (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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621A ARG* 3.4 34.4 - - + +
622A LEU* 1.3 76.2 - - - +
624A PRO* 1.3 65.7 - - - +
625A MET* 4.0 0.3 - - - +
635A PRO* 3.7 15.6 - - + +
636A ALA* 3.3 23.6 - - - +
637A MET* 3.7 24.9 - - + -
638A LEU 4.9 0.7 - - - -
660A ILE* 3.9 0.9 - - - -
661A PHE* 2.7 59.5 + + + +
663A GLU* 2.7 23.2 + - + -
679A PHE* 3.7 32.1 - + - -
686A MET* 3.2 25.5 - - + +
706A TYR* 3.4 26.2 - + - -
762A ASP* 4.2 13.7 - - + -
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Residues in contact with PRO 624 (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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622A LEU 3.5 4.5 - - - +
623A TRP* 1.3 83.6 - - - +
625A MET* 1.3 62.1 + - - +
626A GLN* 3.4 4.6 + - + +
636A ALA* 2.8 43.9 + - + +
637A MET 5.1 0.2 - - - +
638A LEU* 3.4 37.2 - - + -
658A TRP* 3.7 37.9 - - + +
659A THR 3.8 5.4 - - - +
660A ILE* 4.0 10.3 - - + -
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Residues in contact with MET 625 (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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570A VAL* 3.7 18.8 - - + -
575A PHE* 5.0 3.1 - - + -
583A MET* 4.5 4.7 - - - -
584A TYR* 3.5 26.5 - - + +
623A TRP 3.4 2.4 + - - -
624A PRO* 1.3 68.1 - - - +
626A GLN* 1.3 59.3 + - - +
633A LYS* 3.2 40.9 + - + +
634A ARG 3.7 4.0 - - - +
635A PRO* 3.6 29.4 - - - -
655A GLU* 3.9 12.0 - - - +
658A TRP* 4.6 3.5 + - - -
659A THR* 2.8 27.8 + - + +
660A ILE 3.8 1.1 - - - -
661A PHE* 3.3 41.3 - - + +
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Residues in contact with GLN 626 (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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624A PRO* 4.2 5.4 - - + +
625A MET* 1.3 75.0 - - - +
627A ALA* 1.3 74.4 + - - +
628A ARG* 3.9 7.8 + - + +
633A LYS* 3.6 4.1 - - - -
634A ARG 3.0 28.8 + - - +
636A ALA* 3.9 31.4 - - + +
655A GLU* 5.3 3.8 - - - +
761A MET* 4.9 13.1 - - - +
1112C GLY* 5.7 0.4 - - - -
1113C LYS* 3.6 37.4 - - + +
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Residues in contact with ALA 627 (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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625A MET 4.4 0.2 + - - -
626A GLN* 1.3 82.4 - - - +
628A ARG* 1.3 64.6 + - - +
631A GLY* 5.8 1.1 - - - +
632A THR 3.5 8.7 - - - +
633A LYS* 4.3 13.3 - - + +
655A GLU* 5.4 4.2 + - - +
1113C LYS* 3.4 24.0 - - - -
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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