Contacts of the helix formed by residues 694 - 705 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333C GLU* 5.4 0.7 - - - +
673K CYS* 3.1 5.1 - - - +
676K CYS* 3.0 14.8 - - - -
678K THR* 3.5 16.4 - - + -
681K THR* 3.2 21.8 - - - +
683K LEU 4.0 0.2 - - - -
684K TRP* 4.5 2.5 - - - -
685K ARG* 4.0 1.4 - - - -
693K LEU* 1.3 76.5 - - - +
695K ASN* 1.3 67.3 + - - +
696K ALA* 3.1 5.4 - - + +
697K CYS* 3.2 14.1 - - - -
698K GLY* 2.9 20.3 + - - -
708K ARG* 4.3 3.8 - - - -
1713K ZN 1.7 42.4 - - - -
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Residues in contact with ASN 695 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C SER* 3.2 26.7 + - - -
327C GLY* 3.7 9.6 - - - -
328C TRP 5.8 0.2 + - - -
681K THR* 3.2 9.9 + - - +
682K PRO* 3.9 24.4 - - + +
683K LEU* 3.1 35.6 + - - +
685K ARG* 3.0 30.2 + - - +
694K CYS* 1.3 72.3 - - - +
696K ALA* 1.3 54.1 + - - +
699K LEU* 2.8 42.4 + - - +
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Residues in contact with ALA 696 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C HIS* 3.7 14.1 - - + +
325C TRP* 3.6 9.9 - - + -
327C GLY* 3.5 26.2 - - - +
681K THR* 4.7 0.8 + - - +
694K CYS* 3.1 6.6 - - + +
695K ASN* 1.3 76.4 - - - +
697K CYS* 1.3 61.6 + - - +
699K LEU 3.2 0.7 + - - -
700K PHE* 2.8 32.7 + - - +
708K ARG* 3.5 23.1 - - - +
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Residues in contact with CYS 697 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673K CYS* 4.0 4.9 - - - -
675K ASN* 2.9 35.7 - - + +
676K CYS* 3.8 2.0 - - - -
693K LEU* 4.3 9.1 - - + +
694K CYS* 3.2 9.1 + - - +
696K ALA* 1.3 78.4 - - - +
698K GLY* 1.3 63.1 + - - +
700K PHE* 3.7 1.4 - - - +
701K LEU* 3.1 25.6 + - - +
707K VAL* 5.5 0.2 - - - -
708K ARG* 3.6 30.8 + - + +
1713K ZN 2.2 36.1 - - - -
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Residues in contact with GLY 698 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685K ARG* 3.8 18.0 + - - -
693K LEU* 3.9 21.2 - - - +
694K CYS 2.9 16.4 + - - -
697K CYS* 1.3 77.1 - - - +
699K LEU* 1.3 62.0 + - - +
701K LEU* 3.7 3.7 + - - +
702K LYS* 3.1 23.2 + - - +
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Residues in contact with LEU 699 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C TRP* 3.4 26.0 - - + -
326C SER* 3.8 17.7 - - - +
327C GLY* 3.5 20.9 - - - +
685K ARG* 3.7 23.6 - - - +
695K ASN* 2.8 28.6 + - - +
696K ALA 3.7 2.2 - - - +
698K GLY* 1.3 72.7 - - - +
700K PHE* 1.3 65.5 + - - +
702K LYS* 3.0 11.1 + - + +
703K LEU* 2.9 55.5 + - + +
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Residues in contact with PHE 700 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 3.6 40.6 - - + -
28C VAL* 4.1 13.7 - - + -
198C PRO* 4.3 17.9 - - + -
325C TRP* 4.2 9.1 - + + -
696K ALA 2.8 20.8 + - - +
697K CYS 3.7 3.4 - - - +
699K LEU* 1.3 73.6 - - - +
701K LEU* 1.3 58.1 + - - +
703K LEU* 3.2 0.6 + - - -
704K HIS* 2.8 51.8 + + + +
706K VAL* 3.4 34.3 - - + -
708K ARG* 3.4 31.4 - - + -
709K PRO* 3.7 22.2 - - + -
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Residues in contact with LEU 701 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687K ASN* 4.3 21.1 - - - +
688K PRO* 4.8 10.3 - - + -
693K LEU* 4.5 12.8 - - + -
697K CYS 3.1 15.1 + - - +
698K GLY 3.9 4.3 - - - +
700K PHE* 1.3 78.0 - - - +
702K LYS* 1.3 61.0 + - - +
705K GLY* 2.8 49.4 + - - +
706K VAL 3.2 20.6 + - - +
707K VAL* 4.4 13.2 - - + +
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Residues in contact with LYS 702 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685K ARG* 4.5 23.1 - - - +
698K GLY 3.1 15.1 + - - +
699K LEU* 3.0 14.7 + - + +
701K LEU* 1.3 80.9 - - - +
703K LEU* 1.3 74.7 + - + +
705K GLY* 4.5 1.4 + - - -
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Residues in contact with LEU 703 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLN* 4.9 12.6 - - - +
205C LYS* 4.6 6.6 - - - +
324C LEU 5.8 2.0 - - - +
325C TRP* 4.5 12.6 - - + -
699K LEU* 2.9 47.6 + - + +
702K LYS* 1.3 91.9 - - + +
704K HIS* 1.3 86.9 + - + +
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Residues in contact with HIS 704 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS* 5.6 4.2 - - - -
28C VAL* 3.6 29.6 - - + +
198C PRO* 5.1 5.7 + - - +
201C LEU* 3.9 19.5 - - + +
202C GLN* 4.5 9.3 + - - -
205C LYS* 3.1 39.3 + - + +
325C TRP* 6.2 1.0 - + - -
700K PHE* 2.8 51.7 + + + +
703K LEU* 1.3 96.5 + - + +
705K GLY* 1.3 60.7 + - - +
706K VAL* 3.3 8.3 + - - +
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Residues in contact with GLY 705 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701K LEU* 2.8 31.5 + - - +
702K LYS 4.5 1.4 + - - -
703K LEU 3.8 0.6 - - - -
704K HIS* 1.3 77.7 - - - +
706K VAL* 1.3 63.6 + - - +
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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