Contacts of the helix formed by residues 562 - 568 (chain A) 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 SER 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A GLY 4.1 5.2 - - - -
246A SER* 2.7 23.4 + - - -
557A ALA 4.0 1.6 + - - -
558A ALA 2.6 28.8 + - - -
559A VAL* 4.0 1.2 - - - -
561A PHE* 1.3 77.6 - - - +
563A GLN* 1.3 62.5 + - - +
564A MET 3.3 2.6 + - - -
565A ALA* 3.3 7.5 + - - +
566A THR* 3.2 22.2 + - - -
667A TRP* 3.6 39.0 - - - -
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Residues in contact with GLN 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A SER* 3.8 5.2 - - - +
368A HIS* 3.5 24.3 - - + -
369A GLN* 2.9 33.7 + - - +
373A HIS* 4.6 4.7 + - - -
559A VAL 3.8 6.5 - - - +
560A ASN* 3.0 36.0 + - - +
561A PHE 3.2 1.0 - - - -
562A SER* 1.3 79.1 - - - +
564A MET* 1.3 57.8 + - - +
567A TYR* 2.7 41.6 + - + +
610A VAL* 3.6 16.1 - - + +
613A LEU* 3.6 35.7 - - - +
614A THR* 4.3 1.5 - - + +
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Residues in contact with MET 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 4.8 5.6 - - - -
221A ILE* 4.1 24.5 - - + -
223A SER* 3.4 26.7 - - - +
224A GLY 5.4 0.4 - - - +
226A PRO* 3.6 8.0 - - + +
561A PHE 4.6 3.1 + - - +
562A SER 3.3 0.6 - - - -
563A GLN* 1.3 74.7 - - - +
565A ALA* 1.3 62.5 + - - +
566A THR 3.1 1.3 - - - -
568A GLY* 2.8 44.5 + - - -
607A VAL* 4.2 10.8 - - + +
610A VAL* 3.6 16.5 - - + +
611A ASN* 3.7 38.4 - - + +
614A THR* 4.4 13.8 - - + +
667A TRP* 6.2 1.3 - - + -
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Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A PRO* 3.9 15.3 - - + +
227A HIS 5.4 1.3 + - - +
228A ALA* 3.9 22.2 + - - +
237A TRP* 5.2 2.1 - - - -
241A GLN* 5.0 2.2 - - - +
562A SER 3.3 9.3 + - - +
564A MET* 1.3 78.0 - - - +
566A THR* 1.3 60.4 + - - +
568A GLY 4.8 0.2 + - - -
569A PHE 5.4 0.2 + - - -
572A ASN* 4.4 0.5 + - - -
667A TRP* 3.7 30.4 - - + +
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Residues in contact with THR 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 4.6 4.0 + - - +
245A GLY* 3.9 7.1 - - - -
246A SER* 2.8 39.0 + - - +
361A ARG* 4.0 13.7 - - - +
562A SER* 3.2 7.4 + - - -
563A GLN 3.9 2.9 - - - -
564A MET 3.1 0.4 - - - -
565A ALA* 1.3 80.3 - - - +
567A TYR* 1.3 78.4 + - + +
568A GLY 3.6 0.4 - - - -
569A PHE 4.1 0.9 - - - +
572A ASN* 3.0 33.4 + - - +
573A SER* 3.8 20.2 - - - +
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Residues in contact with TYR 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A SER* 4.8 0.4 - - - -
364A ASP* 5.4 0.9 + - - -
365A THR* 3.5 29.5 - - + +
368A HIS* 2.8 41.8 + + - +
369A GLN* 3.5 19.9 + - - -
563A GLN* 2.7 36.5 + - + +
564A MET* 5.3 0.4 - - - -
566A THR* 1.3 86.0 - - + +
568A GLY* 1.3 68.5 + - - +
569A PHE 3.2 5.1 + - - -
570A HIS* 3.7 14.4 + - - +
573A SER* 3.3 40.2 + - - -
575A THR* 4.3 2.2 - - + -
606A MET* 3.8 22.8 - - + +
607A VAL* 5.0 5.7 - - - +
610A VAL* 4.0 16.2 - - + -
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Residues in contact with GLY 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE 4.9 5.4 - - - +
216A LEU* 5.0 2.8 - - - +
217A ILE* 3.9 17.2 - - - +
226A PRO* 3.8 9.6 - - - -
563A GLN 3.9 0.2 + - - -
564A MET* 2.8 40.7 + - - +
566A THR 3.6 0.6 - - - -
567A TYR* 1.3 78.3 - - - +
569A PHE* 1.3 57.4 + - - +
570A HIS* 3.5 2.4 + - - +
607A VAL* 4.3 14.1 - - - +
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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