Contacts of the helix formed by residues 669 - 673 (chain B) in PDB entry 3VF1
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 ILE 669 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.9 4.9 - - + -
651B THR* 4.3 18.2 - - + +
654B ILE* 3.6 31.2 - - + +
655B THR* 5.2 8.3 - - - +
658B ASN* 4.7 2.2 - - - +
666B THR* 3.5 39.5 + - + +
668B LEU* 1.3 75.9 - - - +
670B PRO* 1.3 63.7 - - + +
671B GLY* 3.8 9.9 - - - +
672B HIS* 2.6 56.7 + - + +
673B VAL* 3.3 4.6 + - - +
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Residues in contact with PRO 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.3 9.6 - - + -
623B LEU* 3.7 20.2 + - + +
647B LEU* 3.6 40.6 - - + +
650B ILE* 4.2 14.6 - - + -
651B THR* 3.2 33.2 - - - +
654B ILE* 4.4 0.2 - - + -
668B LEU 3.2 6.9 - - - +
669B ILE* 1.3 82.0 - - + +
671B GLY* 1.3 56.5 + - - +
673B VAL* 3.1 34.0 + - + +
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Residues in contact with GLY 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B PHE* 3.2 32.2 - - - -
651B THR* 4.6 2.4 + - - -
669B ILE* 3.0 7.4 + - - +
670B PRO* 1.3 78.9 - - - +
672B HIS* 1.3 68.3 + - - +
673B VAL 3.5 0.2 - - - -
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Residues in contact with HIS 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.8 51.0 - + - +
98A ASN* 5.7 1.8 + - - -
557B ALA* 4.9 2.4 - - - +
561B PHE* 5.0 4.2 - - - +
616B ILE* 5.0 5.9 - - - +
622B PHE* 3.6 11.8 - - - -
666B THR* 3.3 23.2 + - - +
667B TRP* 5.0 8.6 - - + +
669B ILE* 2.6 39.8 + - + +
671B GLY* 1.3 81.1 - - - -
673B VAL* 1.3 57.9 + - + +
674B PRO* 3.3 11.8 - - - +
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 5.3 0.2 - - + -
553B SER* 3.2 41.1 - - - +
554B CYS* 3.7 14.4 - - - +
557B ALA* 3.7 5.6 - - + -
622B PHE* 3.3 2.8 - - - -
623B LEU* 2.6 40.1 + - + -
667B TRP 3.8 20.4 - - - +
668B LEU* 3.9 18.2 - - + +
669B ILE 3.4 16.8 - - - +
670B PRO* 3.1 8.7 + - + +
671B GLY 3.5 0.2 - - - -
672B HIS* 1.3 78.0 - - - +
674B PRO* 1.3 60.1 - - - +
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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