Contacts of the helix formed by residues 661 - 671 (chain D) in PDB entry 4JVG
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 ASN 661 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659D ILE* 3.6 3.3 - - - +
660D ASN* 1.3 77.5 - - - +
662D ARG* 1.3 66.3 + - - +
663D ASP* 3.2 29.2 + - - +
664D GLN* 3.2 41.8 + - + +
665D ILE* 3.4 13.6 + - - +
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Residues in contact with ARG 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D ILE* 5.6 2.4 - - + +
660D ASN 3.4 6.6 + - - +
661D ASN* 1.3 73.6 + - - +
663D ASP* 1.3 78.4 + - - +
665D ILE* 3.1 31.4 + - + +
666D ILE* 3.4 18.8 - - + +
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Residues in contact with ASP 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661D ASN* 3.2 17.4 + - - +
662D ARG* 1.3 88.1 + - - +
664D GLN* 1.3 66.9 + - - +
665D ILE 3.1 0.9 + - - -
666D ILE* 3.4 19.3 + - + +
667D GLU* 3.3 22.1 + - - +
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Residues in contact with GLN 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D ILE* 4.2 17.7 - - + +
660D ASN 5.3 0.5 + - - -
661D ASN* 3.2 33.6 + - + +
663D ASP* 1.3 79.5 - - - +
665D ILE* 1.3 61.4 + - - +
667D GLU* 3.9 4.1 - - - +
668D MET* 3.0 60.9 + - + +
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Residues in contact with ILE 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D ILE* 4.6 12.3 - - + -
618D LEU* 4.3 22.0 - - + -
656D TYR* 4.2 36.6 - - + +
659D ILE* 3.9 24.7 - - + +
661D ASN 3.4 15.0 - - - +
662D ARG* 3.3 16.8 - - + +
663D ASP 3.0 1.0 - - - -
664D GLN* 1.3 73.4 - - - +
666D ILE* 1.3 70.1 + - + +
668D MET* 3.2 3.9 + - - +
669D VAL* 3.0 33.5 + - + +
674D LEU* 5.1 4.7 - - + -
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Residues in contact with ILE 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D ILE* 3.8 36.3 - - + -
625D ILE* 3.6 33.4 - - + +
662D ARG* 3.4 25.1 - - + +
663D ASP* 3.4 20.8 + - + +
665D ILE* 1.3 77.8 - - + +
667D GLU* 1.3 66.0 + - - +
669D VAL* 3.3 6.8 + - - +
670D GLY* 3.3 10.4 + - - -
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Residues in contact with GLU 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D ASP 3.3 14.7 + - - +
664D GLN* 3.9 5.2 - - - +
665D ILE 3.2 0.2 - - - -
666D ILE* 1.3 82.0 - - - +
668D MET* 1.3 64.4 + - + +
670D GLY* 4.4 0.3 - - - -
671D ARG* 3.2 47.6 + - - +
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Residues in contact with MET 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D ILE* 5.3 4.3 - - + -
664D GLN* 3.0 57.4 + - + +
665D ILE 4.0 1.8 - - - +
667D GLU* 1.3 81.7 - - + +
669D VAL* 1.3 59.6 + - - +
671D ARG* 3.5 31.9 + - - +
672D GLY 3.4 2.3 + - - -
673D SER* 3.1 39.4 + - - +
674D LEU* 3.4 33.4 + - + -
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Residues in contact with VAL 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D MET 4.5 5.4 - - - +
622D PRO* 3.7 22.0 - - + +
625D ILE* 3.5 23.6 - - + -
640D TYR* 5.0 4.7 - - - +
656D TYR* 3.5 33.9 - - + +
665D ILE* 3.0 26.2 + - + +
666D ILE 4.1 2.0 - - - +
668D MET* 1.3 74.3 - - - +
670D GLY* 1.3 67.4 + - - +
671D ARG 3.0 1.9 + - - -
672D GLY* 3.2 11.3 + - - -
674D LEU* 3.9 25.8 - - + +
699D LYS* 5.5 1.7 - - - +
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Residues in contact with GLY 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D PRO* 4.0 24.0 - - - +
625D ILE* 4.4 9.1 - - - +
626D ARG* 3.6 27.2 + - - -
666D ILE 3.3 11.7 + - - -
667D GLU 4.4 0.7 - - - -
669D VAL* 1.3 80.7 - - - +
671D ARG* 1.3 59.4 + - - +
672D GLY* 3.2 1.4 + - - -
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Residues in contact with ARG 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D GLU* 3.2 38.2 + - - +
668D MET* 3.5 31.7 - - - +
669D VAL 3.0 0.8 - - - -
670D GLY* 1.3 78.0 - - - +
672D GLY* 1.3 54.5 + - - +
673D SER* 2.2 41.9 + - - +
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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