Contacts of the helix formed by residues 620 - 630 (chain C) in PDB entry 6VVT
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 GLY 620 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ARG* 5.8 0.2 - - - -
575C ARG* 5.3 9.6 - - - -
619C THR* 1.3 88.4 + - - +
621C MET* 1.3 62.8 + - - +
622C GLU* 3.2 4.9 + - - -
623C LEU* 3.9 10.0 + - - +
624C ARG* 4.3 7.3 + - - +
964C ALA* 4.9 2.7 - - - -
966C PRO* 4.8 3.6 - - - +
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Residues in contact with MET 621 (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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41C VAL* 4.7 7.6 - - - -
44C LEU* 4.1 15.5 - - + -
493C VAL* 4.5 17.3 - - + -
575C ARG* 4.5 21.5 - - - +
580C VAL* 3.5 39.5 - - + +
583C ALA* 3.6 31.9 - - + +
584C MET* 3.5 20.9 - - + -
619C THR* 3.7 1.0 - - - +
620C GLY* 1.3 78.0 - - - +
622C GLU* 1.3 56.3 + - - +
623C LEU 3.3 0.4 - - - -
624C ARG* 3.2 6.6 + - + +
625C ALA* 2.5 44.2 + - + +
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Residues in contact with GLU 622 (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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29C ARG* 4.9 5.4 - - - +
584C MET* 4.0 25.5 - - + +
615C PRO* 4.3 13.2 - - + +
618C GLY* 3.2 10.0 - - - -
619C THR* 2.4 62.6 + - - +
620C GLY 3.1 2.4 + - - -
621C MET* 1.3 71.4 + - - +
623C LEU* 1.3 64.3 + - - +
626C ALA* 3.0 19.4 + - - +
703C GLU* 3.4 25.4 - - + +
704C MET* 3.3 26.3 + - - +
879C ARG* 4.9 1.2 + - - -
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Residues in contact with LEU 623 (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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21C ASN 4.3 9.4 - - - +
23C VAL* 4.0 25.1 - - + -
25C GLY 5.5 0.4 - - - +
26C ALA* 3.3 33.7 - - + -
27C PRO* 3.6 24.7 - - + +
620C GLY 3.9 6.7 + - - +
621C MET 3.3 0.4 - - - -
622C GLU* 1.3 79.8 + - - +
624C ARG* 1.3 63.9 + - + +
627C ILE* 3.3 32.8 + - + +
692C VAL* 5.4 2.5 - - + -
701C ASN 4.3 0.2 - - - +
702C GLY* 3.5 30.2 - - - +
703C GLU* 3.5 10.2 + - + +
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Residues in contact with ARG 624 (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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23C VAL* 4.9 12.8 - - + +
40C GLU* 5.7 8.4 + - - -
41C VAL* 3.2 38.2 + - + +
42C PRO 3.1 25.5 + - - -
43C GLY* 3.8 3.8 - - - +
44C LEU* 4.3 4.6 - - + +
620C GLY 4.3 4.1 + - - +
621C MET* 3.2 22.2 + - + +
623C LEU* 1.3 81.5 - - + +
625C ALA* 1.3 63.3 + - - +
627C ILE* 3.5 17.5 - - - +
628C ASP* 2.6 72.0 + - - +
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Residues in contact with ALA 625 (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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44C LEU* 4.9 1.1 - - - -
437C LEU* 5.6 2.2 - - + -
440C LEU* 3.7 14.5 - - + +
580C VAL* 3.8 27.6 - - + -
584C MET* 4.2 6.5 - - - -
621C MET* 2.5 27.4 + - + +
622C GLU 4.0 2.2 - - - +
624C ARG* 1.3 73.7 - - - +
626C ALA* 1.3 62.6 + - - +
628C ASP* 3.9 1.1 - - - -
629C ALA* 3.1 23.7 + - - +
704C MET* 4.1 13.8 - - + +
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Residues in contact with ALA 626 (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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436C PRO* 5.4 0.7 - - - +
622C GLU 3.0 13.6 + - - +
624C ARG 3.3 0.2 - - - -
625C ALA* 1.3 77.4 - - - +
627C ILE* 1.3 60.3 + - - +
629C ALA* 3.1 18.1 + - - +
630C GLY 3.9 3.1 + - - -
631C ASP 4.5 0.2 + - - -
632C VAL* 4.0 13.4 - - + +
699C THR* 3.8 19.1 - - + -
702C GLY 2.9 27.8 - - - +
704C MET* 3.6 24.8 - - + +
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Residues in contact with ILE 627 (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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23C VAL* 4.8 22.0 - - + -
623C LEU* 3.3 18.6 + - + +
624C ARG* 3.5 25.6 - - - +
626C ALA* 1.3 75.4 - - - +
628C ASP* 1.3 77.6 + - - +
629C ALA 3.6 0.2 + - - -
630C GLY* 3.7 9.9 + - - -
632C VAL* 4.5 12.6 - - + +
634C VAL* 4.6 21.6 - - + +
690C GLY 5.2 5.6 - - - +
692C VAL* 3.7 30.7 - - + -
702C GLY 3.9 7.2 - - - +
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Residues in contact with ASP 628 (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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43C GLY* 3.7 4.0 - - - -
44C LEU* 3.2 41.2 + - + +
45C LEU* 3.1 28.2 - - + +
440C LEU* 4.3 1.7 - - - +
624C ARG* 2.6 57.6 + - - +
625C ALA 4.1 0.2 - - - +
627C ILE* 1.3 85.0 - - - +
629C ALA* 1.3 64.3 + - - +
630C GLY 3.1 3.2 + - - -
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Residues in contact with ALA 629 (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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45C LEU* 4.2 8.6 - - - +
154C LYS* 4.7 5.5 - - - +
431C MET* 5.5 2.6 - - - +
436C PRO* 3.6 39.9 - - + +
440C LEU* 4.3 16.0 + - + +
443C LYS* 4.6 10.0 - - - -
625C ALA 3.1 14.7 + - - +
626C ALA* 3.1 12.5 + - - +
628C ASP* 1.3 78.2 - - - +
630C GLY* 1.3 57.8 + - - +
631C ASP* 3.4 10.1 - - - +
704C MET* 5.4 0.4 - - - -
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Residues in contact with GLY 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 5.3 2.2 - - - -
154C LYS* 3.8 28.8 - - - +
626C ALA 3.9 0.6 + - - -
627C ILE 3.7 10.2 + - - -
628C ASP 3.1 5.3 - - - -
629C ALA* 1.3 77.2 - - - +
631C ASP* 1.3 62.2 - - - +
632C VAL 3.3 13.2 + - - +
664C ARG* 4.3 1.6 + - - -
677C GLN* 5.4 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