Contacts of the strand formed by residues 606 - 610 (chain A) in PDB entry 3GVJ
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 SER 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A TYR* 3.5 27.9 + - - +
594A ILE* 3.3 4.5 - - - +
595A THR* 3.0 37.7 + - - +
604A GLY 4.2 0.2 - - - -
605A SER* 1.3 73.6 - - - +
607A LEU* 1.3 61.2 + - - +
608A HIS* 2.8 26.9 + - - -
620A LEU 3.2 15.9 - - - -
621A ARG* 4.2 8.8 + - - -
622A PHE* 4.0 5.8 - - - -
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Residues in contact with LEU 607 (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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592A TYR* 4.6 3.6 - - + -
593A LEU 3.4 7.4 - - - +
594A ILE* 3.6 22.9 - - + +
606A SER* 1.3 72.7 - - - +
608A HIS* 1.3 79.0 + - - +
619A SER* 3.3 1.2 - - - -
620A LEU* 2.9 41.7 + - + -
622A PHE* 4.0 16.5 - - + -
640A LEU* 3.7 22.2 - - + -
642A MET* 5.0 0.7 - - + -
673A LEU* 3.5 42.6 - - + -
678A TRP* 3.6 23.4 - - + -
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Residues in contact with HIS 608 (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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571A ILE* 3.9 12.0 - - + +
572A PRO* 4.0 10.8 - - + +
575A TYR* 3.4 36.7 - + + +
591A LEU 3.6 0.7 - - - +
592A TYR* 3.3 4.0 - - - -
593A LEU* 2.8 55.5 + - + +
595A THR* 4.5 0.4 - - + +
606A SER* 2.8 28.4 + - - -
607A LEU* 1.3 81.2 - - - +
609A ARG* 1.3 61.4 + - - +
617A TRP* 3.4 24.4 - - + -
618A GLU 3.2 6.5 - - - +
619A SER* 2.8 28.5 + - - -
678A TRP* 4.2 3.6 - - - -
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Residues in contact with ARG 609 (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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590A VAL* 3.8 23.1 - - + -
591A LEU 3.2 4.0 - - - -
592A TYR* 4.0 10.5 + - + -
608A HIS* 1.3 76.3 - - - +
610A SER* 1.3 61.1 + - - +
611A ARG* 4.4 16.1 + - - +
617A TRP* 3.3 4.8 - - - -
618A GLU* 2.9 73.1 + - + +
675A VAL* 2.9 32.7 + - - +
676A ASN* 5.1 2.6 + - - +
678A TRP* 3.5 46.9 - - + +
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Residues in contact with SER 610 (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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586A TYR* 5.5 0.3 - - - -
589A GLY 3.9 0.3 - - - +
590A VAL* 3.5 4.6 - - - -
591A LEU* 2.9 35.4 + - - +
609A ARG* 1.3 73.7 - - - +
611A ARG* 1.3 62.7 + - - +
612A ASP* 2.8 20.3 + - - -
613A ILE 4.4 1.2 + - - -
614A GLY 2.9 19.8 + - - -
616A THR 2.7 26.3 + - - -
617A TRP* 3.7 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
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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