Contacts of the helix formed by residues 493 - 505 (chain A) in PDB entry 2V3V
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 PRO 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ALA* 3.8 12.1 - - + -
466A GLU 5.5 0.9 - - - +
467A ARG* 4.0 30.7 - - + -
487A PRO* 5.2 5.6 - - + -
491A CYS 4.8 0.4 - - - +
492A ARG* 1.3 87.3 - - + +
494A THR* 1.3 65.6 + - - +
495A VAL* 4.5 7.2 - - + +
496A ASN* 3.0 41.1 + - + +
497A THR* 3.1 10.8 + - - -
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Residues in contact with THR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 5.0 0.2 - - + -
116A GLU* 3.4 29.3 + - + +
415A CYS* 4.2 12.9 - - - -
443A ILE* 3.4 41.7 - - + +
461A PRO* 3.8 12.0 - - - +
462A ALA 5.1 1.0 + - - +
467A ARG* 5.2 1.3 + - - +
492A ARG 3.5 1.9 + - - -
493A PRO* 1.3 68.5 - - - +
495A VAL* 1.3 66.0 + - - +
497A THR* 3.9 8.2 + - - -
498A LEU* 2.8 45.2 + - + +
811A MGD 5.1 1.2 + - - -
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Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 5.5 2.9 - - + -
115A GLU* 4.0 14.8 - - + +
116A GLU* 3.6 36.1 - - + +
119A VAL* 4.7 7.0 - - + +
493A PRO* 3.2 6.4 - - + -
494A THR* 1.3 79.3 - - - +
496A ASN* 1.3 63.8 + - - +
498A LEU* 3.6 7.5 + - - +
499A VAL* 3.3 27.5 + - + +
514A PHE* 5.0 1.3 - - + +
516A ASN* 4.1 19.5 - - - +
517A ALA* 4.4 11.0 - - + +
520A VAL* 4.0 21.8 - - + -
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Residues in contact with ASN 496 (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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492A ARG* 5.6 4.3 - - + -
493A PRO* 3.0 41.0 + - + +
495A VAL* 1.3 76.4 - - - +
497A THR* 1.3 66.5 + - - +
499A VAL* 3.4 8.3 + - - +
500A GLU* 3.0 24.1 + - - +
514A PHE 4.9 2.1 - - - +
515A ARG 3.0 28.9 + - - +
516A ASN* 4.3 4.9 + - - +
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Residues in contact with THR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.5 27.8 - - + -
85A LEU* 4.2 7.7 - - + +
88A MET* 5.6 0.9 - - + -
443A ILE* 4.9 5.8 - - + -
459A LEU* 3.7 30.7 - - + -
492A ARG* 4.1 11.8 + - - +
493A PRO 3.1 13.4 + - - -
494A THR* 3.5 15.2 + - - +
496A ASN* 1.3 75.2 - - - +
498A LEU* 1.3 65.7 + - + +
500A GLU* 3.3 6.2 + - - +
501A PHE* 3.0 29.1 + - + +
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Residues in contact with LEU 498 (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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88A MET* 5.5 1.8 - - + -
106A TRP* 3.9 23.3 - - + -
116A GLU* 3.4 29.8 - - - +
119A VAL* 3.9 11.7 - - + -
120A ALA* 3.9 15.3 - - + +
123A ILE* 3.4 17.2 - - + +
413A ILE* 5.0 4.9 - - + -
443A ILE* 4.2 9.9 - - + -
494A THR* 2.8 42.6 + - + +
495A VAL* 3.7 4.5 - - - +
497A THR* 1.3 77.2 - - + +
499A VAL* 1.3 56.0 + - - +
501A PHE* 3.4 14.2 + - + +
502A ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 499 (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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119A VAL* 4.2 11.9 - - + -
495A VAL* 3.3 17.5 + - + +
496A ASN* 3.4 9.6 + - - +
498A LEU* 1.3 75.8 - - - +
500A GLU* 1.3 62.4 + - - +
502A ALA* 3.5 2.1 + - - +
503A ARG* 3.1 50.0 + - - +
512A VAL* 3.5 41.2 - - + +
514A PHE* 4.0 28.0 - - + +
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Residues in contact with GLU 500 (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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85A LEU* 3.8 16.8 - - + -
492A ARG* 5.9 1.8 - - - +
496A ASN 3.0 17.3 + - - +
497A THR* 3.9 3.6 - - - +
499A VAL* 1.3 74.5 - - - +
501A PHE* 1.3 64.6 + - - +
503A ARG* 3.4 26.3 + - - +
504A ARG* 2.6 76.8 + - - +
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Residues in contact with PHE 501 (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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85A LEU* 4.2 17.3 - - + +
88A MET* 3.6 43.1 - - + -
89A ALA* 4.1 12.6 - - - -
92A PHE* 3.9 29.8 - + + -
123A ILE* 4.2 13.0 - - + -
124A PHE* 4.6 2.5 - + - -
128A PHE* 3.7 34.1 - + - -
413A ILE* 3.9 19.1 - - + -
497A THR* 3.0 17.7 + - + +
498A LEU* 3.6 13.7 - - + +
500A GLU* 1.3 74.8 - - - +
502A ALA* 1.3 68.5 + - - +
504A ARG* 3.4 4.5 + - - +
505A ALA* 2.8 36.2 + - + +
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Residues in contact with ALA 502 (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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123A ILE* 3.6 27.8 - - + -
498A LEU 2.9 18.4 + - - +
499A VAL 3.7 5.2 - - - +
500A GLU 3.4 0.2 - - - -
501A PHE* 1.3 79.9 - - - +
503A ARG* 1.3 61.2 + - - +
505A ALA* 3.2 9.3 + - - -
506A GLY 3.3 0.3 + - - -
507A VAL* 3.1 41.5 + - + +
512A VAL* 3.7 14.6 - - + -
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Residues in contact with ARG 503 (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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499A VAL* 3.1 44.3 + - - +
500A GLU* 3.4 29.7 + - - +
502A ALA* 1.3 76.1 - - - +
504A ARG* 1.3 63.9 + - + +
506A GLY* 3.2 14.2 + - - -
507A VAL 4.4 8.8 + - - +
509A PRO* 5.0 20.4 + - + +
512A VAL* 4.2 18.7 + - + +
513A ASN* 5.5 4.8 + - - +
514A PHE 4.8 6.5 + - - +
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Residues in contact with ARG 504 (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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82A ASP* 3.1 49.3 + - - +
85A LEU* 3.6 22.5 - - - +
86A ASP* 3.1 26.7 + - - +
89A ALA* 3.6 22.6 - - + +
93A ARG* 5.6 0.5 - - - +
500A GLU* 2.6 65.1 + - - +
501A PHE 3.9 0.4 - - - +
503A ARG* 1.3 78.7 - - + +
505A ALA* 1.3 58.7 + - - +
506A GLY 3.2 2.1 + - - -
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Residues in contact with ALA 505 (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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89A ALA* 3.8 28.0 - - + +
93A ARG* 2.8 44.8 + - + +
128A PHE* 4.1 24.9 - - + -
501A PHE* 2.8 22.3 + - + +
502A ALA 3.2 4.4 + - - +
504A ARG* 1.3 75.9 - - - +
506A GLY* 1.3 51.9 + - - +
507A VAL 3.4 1.7 + - - -
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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