Contacts of the strand formed by residues 592 - 599 (chain C) in PDB entry 6VSB
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 PHE 592 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A MET* 3.4 44.2 - - + -
855A PHE* 4.2 13.7 - - - -
857A GLY* 4.0 14.1 - - - -
858A LEU 5.5 2.7 - - - -
317C ASN* 3.7 9.4 - - - +
318C PHE* 3.1 27.6 - - - +
319C ARG* 3.8 15.5 - - + +
589C PRO* 4.4 22.2 - - + -
590C CYS 3.5 14.1 - - - +
591C SER* 1.3 76.1 - - - +
593C GLY* 1.3 64.4 + - - +
614C ASP* 4.8 4.5 - - - +
615C VAL* 4.5 8.5 - - - +
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Residues in contact with GLY 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C ASN* 2.8 15.7 + - - +
318C PHE* 2.8 43.7 + - - -
592C PHE* 1.3 83.6 - - - +
594C GLY* 1.3 60.3 + - - -
613C GLN 4.8 5.2 - - - -
614C ASP* 5.1 3.4 - - - -
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Residues in contact with GLY 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859A THR* 6.3 0.6 - - - +
314C GLN* 5.6 6.1 - - - -
316C SER 3.9 7.4 - - - -
317C ASN* 3.6 7.4 - - - +
318C PHE* 3.5 5.5 - - - -
593C GLY* 1.3 73.4 - - - -
595C VAL* 1.3 56.0 + - - -
613C GLN* 2.7 59.9 + - - +
614C ASP* 5.6 0.4 + - - -
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Residues in contact with VAL 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C PRO* 6.4 0.4 - - + -
298C GLU* 5.4 3.8 - - - +
314C GLN* 3.9 3.8 - - - +
315C THR* 3.4 26.8 + - - +
316C SER* 3.2 27.8 + - - +
317C ASN 4.1 9.9 - - - +
318C PHE* 3.9 8.1 - - + -
594C GLY* 1.3 74.1 - - - -
596C SER* 1.3 63.7 + - - +
597C VAL* 5.5 2.5 - - + -
610C VAL* 3.5 30.1 - - + -
611C LEU 3.2 6.3 - - - +
612C TYR* 3.6 20.6 - - + -
613C GLN* 5.2 0.4 - - - -
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Residues in contact with SER 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ILE* 3.0 31.0 - - - +
313C TYR 2.6 29.3 + - - -
314C GLN* 3.4 3.3 + - - +
594C GLY 4.3 0.2 - - - -
595C VAL* 1.3 74.4 - - - +
597C VAL* 1.3 60.3 + - - +
610C VAL* 3.5 5.0 - - - +
611C LEU* 2.7 49.7 + - - +
613C GLN* 4.3 18.1 + - - +
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Residues in contact with VAL 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C PRO* 3.9 25.6 - - + +
299C THR* 3.3 34.8 - - + -
311C GLY 3.6 1.6 - - - +
312C ILE* 3.3 8.5 - - - +
313C TYR* 2.9 43.4 + - + +
315C THR* 4.1 10.8 - - + +
595C VAL* 5.5 2.5 - - + -
596C SER* 1.3 78.3 - - - +
598C ILE* 1.3 61.9 + - - +
599C THR* 4.1 5.2 - - + -
608C VAL* 4.0 13.9 - - + -
609C ALA 3.4 4.9 - - - +
610C VAL* 4.8 4.7 - - + -
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Residues in contact with ILE 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C GLY 4.0 1.3 - - - -
312C ILE* 3.6 41.5 - - + -
597C VAL* 1.3 71.1 - - - +
599C THR* 1.3 70.0 + - - +
600C PRO* 4.6 0.9 - - - +
608C VAL* 3.4 2.1 - - - -
609C ALA* 2.6 55.6 + - + +
611C LEU* 4.9 4.0 - - + -
650C LEU* 4.5 10.1 - - + -
664C ILE* 3.8 18.4 - - + -
666C ILE* 4.0 23.1 - - + -
672C ALA* 3.6 26.9 - - + -
692C ILE* 4.6 8.7 - - + +
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Residues in contact with THR 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C LEU* 4.5 15.7 - - + -
299C THR* 5.6 1.3 - - + -
308C VAL* 4.7 4.7 + - + +
309C GLU 3.7 13.0 + - - -
310C LYS* 3.9 3.3 - - - +
311C GLY 3.4 29.4 + - - +
313C TYR* 4.4 5.2 - - + -
597C VAL* 4.6 11.4 - - + +
598C ILE* 1.3 84.5 - - - +
600C PRO* 1.3 68.0 - - - +
601C GLY* 3.4 19.2 + - - +
607C GLN 4.3 3.1 - - - +
608C VAL* 3.6 23.1 - - + -
664C ILE* 4.0 9.0 - - - +
692C ILE* 5.0 0.7 - - - -
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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