Contacts of the helix formed by residues 694 - 705 (chain O) in PDB entry 2VUU
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 CYS 694 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G HIS* 5.7 0.9 - - - -
333G GLU* 5.6 1.8 - - - +
673O CYS* 3.5 6.7 - - - -
676O CYS* 3.4 5.2 - - - -
678O THR* 3.4 23.3 - - + -
680O THR 5.2 0.2 - - - +
681O THR* 3.4 13.5 - - - +
684O TRP* 3.7 11.9 - - - -
685O ARG* 3.8 0.2 - - - +
693O LEU* 1.3 78.8 - - - +
695O ASN* 1.3 65.3 + - - +
696O ALA* 3.6 11.9 - - - -
697O CYS* 3.2 18.6 - - - -
698O GLY* 3.0 16.5 + - - -
708O ARG* 4.7 0.9 - - - -
1712O ZN 2.2 36.3 - - - -
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Residues in contact with ASN 695 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326G SER* 3.1 27.7 + - - -
327G GLY* 3.8 6.8 - - - -
681O THR* 2.9 15.9 + - - +
682O PRO* 4.3 16.2 - - + +
683O LEU* 3.1 33.8 + - - +
685O ARG* 3.0 37.6 + - - +
694O CYS* 1.3 71.0 - - - +
696O ALA* 1.3 57.4 + - - +
699O LEU* 2.8 40.2 + - - +
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Residues in contact with ALA 696 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G HIS* 3.8 15.7 - - + +
325G TRP* 3.7 8.5 - - + -
327G GLY* 3.4 26.8 - - - +
681O THR* 4.6 0.4 + - - -
694O CYS* 3.1 10.0 - - - -
695O ASN* 1.3 77.7 - - - +
697O CYS* 1.3 58.8 + - - +
699O LEU* 3.1 1.6 + - - +
700O PHE* 2.8 32.4 + - - +
708O ARG* 3.7 19.5 - - - +
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Residues in contact with CYS 697 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673O CYS* 4.2 4.9 - - - -
675O ASN* 3.5 32.3 - - + -
676O CYS* 3.7 7.9 - - - -
693O LEU* 4.3 9.5 - - + +
694O CYS* 3.2 6.8 - - - +
696O ALA* 1.3 79.1 - - - +
698O GLY* 1.3 62.8 + - - +
700O PHE* 3.6 1.6 + - - +
701O LEU* 3.1 25.3 + - - +
707O VAL* 5.5 0.3 - - - -
708O ARG* 3.6 29.1 + - + +
1712O ZN 2.3 34.1 - - - -
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Residues in contact with GLY 698 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685O ARG* 3.9 18.5 - - - -
693O LEU* 3.9 21.6 - - - +
694O CYS 3.0 15.1 + - - -
697O CYS* 1.3 75.6 - - - +
699O LEU* 1.3 64.0 + - - +
701O LEU* 3.8 3.0 - - - +
702O LYS* 3.0 24.4 + - - +
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Residues in contact with LEU 699 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G TRP* 4.0 11.0 - - + -
326G SER* 3.1 31.6 - - - +
327G GLY* 3.7 22.0 - - - +
685O ARG* 3.7 29.7 - - - +
695O ASN* 2.8 23.4 + - - +
696O ALA 3.6 3.1 - - - +
698O GLY* 1.3 72.0 - - - +
700O PHE* 1.3 61.3 + - - +
702O LYS* 3.1 9.8 + - + +
703O LEU* 2.9 62.2 + - + +
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Residues in contact with PHE 700 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.4 33.4 - - + -
28G VAL* 3.9 15.7 - - + -
198G PRO* 4.5 14.4 - - + -
325G TRP* 4.2 12.0 - + + -
696O ALA 2.8 20.2 + - - +
697O CYS 3.8 3.8 - - - +
699O LEU* 1.3 73.7 - - - +
701O LEU* 1.3 55.8 + - - +
703O LEU* 4.8 0.4 - - - -
704O HIS* 2.9 48.3 + + + +
706O VAL* 3.1 41.7 - - + -
708O ARG* 3.3 31.9 - - + -
709O PRO* 3.5 28.9 - - + -
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Residues in contact with LEU 701 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687O ASN* 5.5 5.6 - - + -
688O PRO* 5.6 6.5 - - + -
693O LEU* 4.5 19.3 - - + -
697O CYS 3.1 15.2 + - - +
698O GLY 3.8 3.6 - - - +
700O PHE* 1.3 79.8 - - - +
702O LYS* 1.3 59.7 + - - +
705O GLY* 2.8 37.8 + - - +
706O VAL* 3.2 37.2 - - - +
707O VAL* 3.5 17.3 - - + +
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Residues in contact with LYS 702 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685O ARG* 3.6 28.0 - - - +
698O GLY 3.0 17.4 + - - +
699O LEU* 3.1 12.5 + - + +
701O LEU* 1.3 79.7 - - - +
703O LEU* 1.3 70.7 + - + +
705O GLY 4.5 1.4 + - - -
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Residues in contact with LEU 703 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G GLN* 4.7 15.9 - - - +
205G LYS* 3.1 22.5 + - - +
324G LEU 6.0 0.2 - - - +
325G TRP* 4.3 18.6 - - + -
699O LEU* 2.9 42.7 + - + +
700O PHE 4.0 2.5 - - - +
702O LYS* 1.3 91.5 - - + +
704O HIS* 1.3 73.2 + - + +
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Residues in contact with HIS 704 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 4.8 13.6 + - - +
28G VAL* 3.5 29.8 - - + +
198G PRO* 5.1 5.1 + - - +
201G LEU* 3.8 29.6 - - + +
202G GLN* 5.0 7.1 + - - -
205G LYS* 3.1 42.4 + - + +
325G TRP* 5.9 2.6 - + - -
700O PHE* 2.9 51.1 + + + +
703O LEU* 1.3 86.9 - - + +
705O GLY* 1.3 61.7 + - - +
706O VAL* 3.3 5.4 + - - +
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Residues in contact with GLY 705 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701O LEU* 2.8 32.6 + - - +
702O LYS 4.5 1.6 + - - -
703O LEU 3.8 0.4 - - - -
704O HIS* 1.3 73.5 - - - +
706O VAL* 1.3 64.8 + - - +
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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