Contacts of the helix formed by residues 660 - 670 (chain D) in PDB entry 5IJO
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 ALA 660 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655D LYS 5.2 9.0 - - - +
657D PRO 3.6 10.8 + - - +
658D GLU 2.6 12.0 + - - +
659D ILE* 1.3 73.9 - - - +
661D ALA* 1.3 51.9 + - - +
662D SER 3.3 1.3 - - - -
663D LEU* 2.7 39.6 + - + +
664D TRP* 3.2 7.5 + - + +
714D LEU* 5.5 11.7 - - + +
718D SER* 4.9 18.8 - - - +
719D PHE* 5.4 5.6 - - + -
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Residues in contact with ALA 661 (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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658D GLU 3.7 7.4 + - - +
659D ILE* 3.3 3.2 - - - -
660D ALA* 1.3 78.0 - - - +
662D SER* 1.3 64.0 + - - +
664D TRP* 3.2 7.3 + - - +
665D GLN* 3.1 23.7 + - - +
720D PRO* 5.0 17.0 - - + -
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Residues in contact with SER 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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659D ILE 4.7 4.9 + - - -
660D ALA 3.1 1.0 + - - -
661D ALA* 1.3 78.5 - - - +
663D LEU* 1.3 63.3 + - - +
665D GLN* 3.4 6.4 + - - +
666D SER* 3.1 21.7 + - - -
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Residues in contact with LEU 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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654D GLY* 5.8 7.9 - - - -
659D ILE 5.8 0.2 - - - +
660D ALA* 2.7 23.1 + - + +
662D SER* 1.3 71.6 - - - +
664D TRP* 1.3 63.4 + - - +
666D SER* 3.1 8.3 + - - +
667D LEU* 3.1 22.4 + - - +
714D LEU* 5.8 7.4 - - + -
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Residues in contact with TRP 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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660D ALA* 3.2 10.4 + - + +
661D ALA* 3.2 9.1 + - - +
663D LEU* 1.3 77.5 - - - +
665D GLN* 1.3 64.3 + - - +
667D LEU* 3.2 6.9 + - - +
668D GLU* 2.9 25.9 + - - +
714D LEU* 6.0 8.2 - - + +
719D PHE* 5.0 17.5 - - + -
720D PRO* 5.2 9.4 - - + -
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Residues in contact with GLN 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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661D ALA 3.1 15.9 + - - +
662D SER* 3.8 6.1 - - - +
664D TRP* 1.3 76.1 - - - +
666D SER* 1.3 64.1 + - - +
668D GLU* 3.9 4.8 - - - +
669D TYR* 2.9 28.5 + - + +
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Residues in contact with SER 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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631D LEU* 4.6 21.1 - - - -
662D SER 3.1 14.1 + - - -
663D LEU* 3.1 11.2 + - - -
665D GLN* 1.3 76.7 - - - +
667D LEU* 1.3 52.2 + - - +
669D TYR* 3.6 4.4 - - - +
670D THR* 2.6 43.3 + - - -
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Residues in contact with LEU 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 LEU 3.1 12.1 + - - +
664D TRP* 3.6 9.4 - - - +
666D SER* 1.3 75.3 - - - +
668D GLU* 1.3 67.0 + - - +
670D THR* 3.2 21.5 + - - +
672D ILE* 4.1 7.1 - - - +
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Residues in contact with GLU 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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664D TRP 2.9 16.2 + - - +
665D GLN* 4.0 4.3 - - - +
667D LEU* 1.3 76.7 - - - +
669D TYR* 1.3 63.6 + - - +
672D ILE* 4.0 4.4 - - - +
673D LEU* 3.0 32.2 + - + +
723D LEU* 5.9 4.3 - - + -
724D GLY* 5.1 17.5 - - - +
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Residues in contact with TYR 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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665D GLN* 2.9 19.8 + - + +
666D SER* 3.7 3.8 - - - +
668D GLU* 1.3 78.9 - - - +
670D THR* 1.3 57.3 + - - +
673D LEU* 4.5 4.9 - - - -
674D GLN* 3.2 36.1 + - + +
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Residues in contact with THR 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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631D LEU* 5.5 7.0 - - - -
634D LEU* 5.8 5.8 - - - -
635D GLN* 5.8 9.2 - - - -
666D SER* 2.6 26.5 + - - -
667D LEU* 3.2 12.4 + - - +
669D TYR* 1.3 75.1 - - - +
672D ILE* 2.6 34.3 + - - +
674D GLN* 5.2 3.1 - - - -
697D ARG* 5.1 4.7 - - - +
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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