Contacts of the helix formed by residues 694 - 705 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D HIS* 5.4 0.7 - - - -
333D GLU* 5.9 1.6 - - - +
673L CYS* 3.5 4.5 - - - +
676L CYS* 3.7 2.5 - - - -
678L THR* 3.4 21.5 - - + -
681L THR* 3.9 13.9 - - - +
684L TRP* 4.6 1.3 - - - -
685L ARG* 4.0 1.0 - - - +
693L LEU* 1.3 76.1 - - - +
695L ASN* 1.3 65.6 + - - +
696L ALA* 3.3 15.0 - - - -
697L CYS* 2.1 58.3 - - - -
698L GLY* 2.9 21.0 + - - -
708L ARG* 4.2 2.0 - - - -
1713L ZN 2.3 21.9 - - - -
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Residues in contact with ASN 695 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D SER 3.0 26.7 + - - -
327D GLY* 3.3 15.1 - - - -
328D TRP 5.3 1.0 + - - -
681L THR* 3.0 16.3 + - - +
682L PRO* 4.0 21.0 - - + +
683L LEU* 3.0 35.0 + - + +
685L ARG* 2.9 37.8 + - - +
694L CYS* 1.3 69.4 - - - +
696L ALA* 1.3 53.6 + - - +
699L LEU* 2.8 40.0 + - - +
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Residues in contact with ALA 696 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D HIS* 3.5 20.6 - - + +
325D TRP* 3.6 11.2 - - + -
327D GLY* 3.3 26.9 + - - +
681L THR* 4.6 0.6 + - - -
694L CYS* 3.1 12.2 - - - -
695L ASN* 1.3 77.5 - - - +
697L CYS* 1.3 60.0 + - - +
699L LEU 3.2 0.3 + - - -
700L PHE* 2.8 33.6 + - - +
708L ARG* 3.5 11.0 - - - +
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Residues in contact with CYS 697 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673L CYS* 3.4 1.8 - - - -
675L ASN* 4.1 13.2 - - + +
676L CYS* 3.2 10.3 - - - -
693L LEU* 4.0 17.9 - - + -
694L CYS* 2.1 34.7 - - - +
696L ALA* 1.3 70.8 - - - +
698L GLY* 1.3 62.6 + - - +
700L PHE* 3.6 1.7 - - - +
701L LEU* 3.0 25.3 + - - +
707L VAL* 5.6 0.2 - - - -
708L ARG* 3.8 24.9 + - - +
1713L ZN 1.8 44.6 - - - -
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Residues in contact with GLY 698 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685L ARG* 4.0 17.8 - - - -
687L ASN* 5.5 2.1 - - - +
693L LEU* 3.8 21.2 - - - +
694L CYS 2.9 15.8 + - - -
695L ASN 4.0 0.2 - - - -
697L CYS* 1.3 77.6 - - - +
699L LEU* 1.3 56.8 + - - +
701L LEU* 3.7 2.6 + - - +
702L LYS* 3.0 28.4 + - - +
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Residues in contact with LEU 699 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D TRP* 3.4 16.2 - - + -
326D SER* 3.9 19.3 - - - +
327D GLY* 3.8 27.6 - - - +
685L ARG* 3.9 31.1 - - - +
695L ASN* 2.8 24.2 + - - +
696L ALA 3.7 2.5 - - - +
698L GLY* 1.3 71.1 - - - +
700L PHE* 1.3 67.2 + - - +
702L LYS* 3.2 8.2 + - + +
703L LEU* 3.0 51.7 + - + +
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Residues in contact with PHE 700 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 3.4 37.7 - - + -
28D VAL* 4.0 13.5 - - + -
198D PRO* 4.3 14.4 - - + -
201D LEU* 4.7 0.2 - - + -
325D TRP* 4.3 6.5 - + + -
696L ALA 2.8 21.6 + - - +
697L CYS 3.6 3.8 - - - +
699L LEU* 1.3 73.7 - - - +
701L LEU* 1.3 66.1 + - - +
703L LEU 3.2 1.0 + - - -
704L HIS* 2.8 49.0 + + + +
706L VAL* 3.2 38.4 - - + -
707L VAL 3.6 2.0 - - - -
708L ARG* 3.2 29.6 - - + -
709L PRO* 3.4 28.5 - - + -
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Residues in contact with LEU 701 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687L ASN* 3.7 39.9 - - + +
691L GLN* 5.3 1.8 - - - +
693L LEU* 4.6 11.9 - - + -
697L CYS 3.0 15.0 + - - +
698L GLY 3.9 4.5 - - - +
700L PHE* 1.3 77.3 - - - +
702L LYS* 1.3 62.0 + - - +
705L GLY* 2.6 64.0 + - - +
706L VAL* 3.4 20.9 - - - +
707L VAL* 4.0 14.4 - - + +
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Residues in contact with LYS 702 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685L ARG* 4.3 20.7 - - - +
687L ASN* 5.1 6.5 + - - +
698L GLY 3.0 16.7 + - - +
699L LEU* 3.4 7.6 - - + +
701L LEU* 1.3 83.7 - - - +
703L LEU* 1.3 75.2 + - + +
705L GLY 4.6 0.7 + - - -
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Residues in contact with LEU 703 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLN* 4.5 18.6 - - - +
205D LYS* 3.9 12.3 + - - +
324D LEU 5.6 2.7 - - - +
325D TRP* 4.9 6.3 - - + -
699L LEU* 3.0 43.9 + - + +
700L PHE 4.0 1.6 - - - +
702L LYS* 1.3 95.0 - - + +
704L HIS* 1.3 80.8 + - + +
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Residues in contact with HIS 704 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 5.6 5.0 + - - -
28D VAL* 3.5 31.0 - - + +
198D PRO* 5.0 6.8 + - - +
201D LEU* 3.5 32.1 - - + +
202D GLN* 4.8 7.8 + - - -
205D LYS* 3.1 34.4 + - + +
325D TRP* 5.9 2.4 - - - -
700L PHE* 2.8 57.4 + + + +
703L LEU* 1.3 87.9 - - + +
705L GLY* 1.3 61.7 + - - +
706L VAL* 3.4 6.1 + - - +
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Residues in contact with GLY 705 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701L LEU* 2.6 35.8 + - - +
702L LYS 4.6 0.8 + - - -
703L LEU 3.8 0.6 - - - -
704L HIS* 1.3 72.7 - - - +
706L VAL* 1.3 64.2 + - - +
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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