Contacts of the strand formed by residues 630 - 635 (chain G) in PDB entry 6MZL
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 VAL 630 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589G TRP* 3.4 19.2 - - - +
603G GLY* 3.7 22.7 - - - +
604G GLY 2.9 26.2 + - - +
607G ARG* 4.5 7.6 - - - +
608G VAL 3.3 23.8 - - - +
626G HIS* 4.6 5.8 - - - +
628G ALA 3.2 7.7 + - - +
629G ASP* 1.3 72.6 - - - +
631G ASN* 1.3 65.4 + - - +
632G CYS 3.8 11.2 - - - +
633G THR* 4.5 1.1 - - + -
644G THR* 3.7 31.9 - - + -
646G SER* 3.6 9.4 - - - +
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Residues in contact with ASN 631 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589G TRP* 4.0 10.8 - - - +
590G ASP* 3.3 18.2 - - - +
629G ASP* 3.5 7.4 + - - +
630G VAL* 1.3 78.6 - - - +
632G CYS* 1.3 61.4 + - + +
645G GLY 2.8 14.2 + - - +
646G SER 3.0 25.4 + - - -
647G ALA* 3.6 8.1 - - - +
671G PRO* 4.3 5.5 - - - +
672G ILE 2.5 33.0 + - - +
673G HIS* 4.8 1.8 + - - -
60I MET* 3.3 35.2 - - + +
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Residues in contact with CYS 632 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590G ASP* 3.3 8.1 - - - +
630G VAL* 3.8 0.9 - - - +
631G ASN* 1.3 78.0 - - + +
633G THR* 1.3 67.6 + - - +
634G ARG* 5.5 7.0 - - + -
644G THR* 3.4 3.5 - - - +
645G GLY* 2.9 47.2 + - - +
672G ILE* 4.4 7.0 - - - -
673G HIS 4.8 11.2 - - - +
674G SER* 4.3 6.7 - - - +
675G LEU* 3.6 36.6 - - + +
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Residues in contact with THR 633 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590G ASP* 2.4 48.6 + - + +
592G GLN* 3.4 13.5 - - - +
601G VAL* 3.7 21.8 - - + +
602G SER 4.3 1.6 - - - -
603G GLY* 3.4 34.5 - - - +
609G ALA* 4.9 4.2 - - - +
630G VAL* 4.5 1.1 - - + -
632G CYS* 1.3 74.6 - - - +
634G ARG* 1.3 64.5 + - - +
642G VAL* 4.7 3.8 - - - +
643G ALA 3.1 8.7 + - - -
644G THR* 3.2 22.2 + - - -
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Residues in contact with ARG 634 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590G ASP* 4.4 5.4 - - - +
592G GLN* 3.4 37.3 + - + +
601G VAL* 4.8 0.2 - - - -
632G CYS* 5.5 6.2 - - + -
633G THR* 1.3 81.9 + - - +
635G PHE* 1.3 70.1 + - - +
642G VAL* 3.4 5.1 - - - -
643G ALA* 2.9 35.0 + - - +
675G LEU* 3.6 22.9 + - + +
676G THR* 3.4 31.4 - - - +
677G PHE* 3.7 12.2 - - + +
718G ARG* 3.2 33.7 - - - +
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Residues in contact with PHE 635 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592G GLN* 3.1 26.9 - - + +
593G PHE 3.1 16.8 - - - +
594G SER* 3.1 35.2 - - - -
595G PRO* 3.7 9.0 - - + -
599G TYR* 4.9 2.0 - - + -
600G PHE* 3.7 9.9 - - - -
601G VAL* 3.5 28.5 - - + -
611G LEU* 4.1 11.4 - - + -
634G ARG* 1.3 82.9 + - - +
636G HIS* 1.3 70.2 + - - +
637G PRO* 4.0 1.2 - - - +
639G SER* 3.6 32.5 - - - -
641G TYR 3.3 3.4 - - - -
642G VAL* 3.7 13.5 - - + -
677G PHE* 3.2 17.3 - - - +
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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
------------------------------------------------------------
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