Contacts of the helix formed by residues 626 - 632 (chain A) in PDB entry 2Z5U
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 626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A FAJ 3.4 43.1 - - + +
316A ARG* 3.4 24.0 - - - +
624A THR 4.3 0.2 - - - +
625A LEU* 1.3 85.2 - - - +
627A LEU* 1.3 66.3 + - - +
628A GLY 3.1 0.9 - - - +
629A VAL* 2.9 23.7 + - + +
630A LEU* 3.2 9.4 + - - +
656A PHE* 4.3 0.9 - - + -
756A TRP 3.6 22.2 - - - +
757A ALA* 3.9 20.0 - - - +
802A HIS* 4.4 2.0 - - + -
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Residues in contact with LEU 627 (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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316A ARG* 4.7 0.2 - - - +
625A LEU 3.5 1.4 + - - -
626A PRO* 1.3 72.4 - - - +
628A GLY* 1.3 56.8 - - - +
630A LEU* 3.2 5.1 + - + -
631A LYS* 3.0 42.3 + - + +
651A VAL* 3.9 39.0 - - + +
654A MET* 3.7 33.7 - - + +
655A GLY 3.5 27.1 - - - +
656A PHE* 3.5 19.7 - - + -
762A SER* 4.0 3.8 - - - -
776A MET* 4.7 2.7 - - - -
802A HIS* 3.9 29.3 + - + -
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Residues in contact with GLY 628 (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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626A PRO 3.1 1.4 - - - -
627A LEU* 1.3 80.1 - - - +
629A VAL* 1.3 59.8 + - - +
631A LYS* 3.5 7.2 + - - +
632A GLN* 3.3 16.8 + - - +
656A PHE* 3.4 31.2 - - - -
757A ALA 3.7 6.9 + - - -
758A ARG* 3.6 20.4 - - - +
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Residues in contact with VAL 629 (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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1A FAJ 4.7 7.2 - - + +
625A LEU* 4.5 14.6 - - + -
626A PRO* 2.9 21.2 + - + +
628A GLY* 1.3 75.9 - - - +
630A LEU* 1.3 62.8 + - - +
632A GLN* 3.2 22.5 + - - +
635A PRO* 5.5 0.3 - - - +
636A ALA* 3.9 26.5 + - + +
637A VAL* 4.4 13.9 + - + -
755A PRO 3.7 22.4 - - - +
756A TRP* 3.9 21.8 - - - +
757A ALA 3.9 4.9 + - - +
758A ARG* 4.4 3.4 - - + -
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Residues in contact with LEU 630 (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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623A CYS* 4.3 3.8 - - - -
625A LEU* 3.7 36.8 - - + +
626A PRO 3.2 9.2 + - - +
627A LEU* 3.6 8.3 - - - +
629A VAL* 1.3 78.1 - - - +
631A LYS* 1.3 56.9 + - - +
632A GLN 3.8 2.5 + - - +
635A PRO* 6.2 0.2 - - - +
639A PHE* 4.1 20.9 - - + -
643A LEU* 5.2 5.2 - - + -
651A VAL* 3.7 30.4 - - + +
776A MET* 5.0 2.7 - - - -
798A PHE* 5.0 14.8 - - + -
802A HIS* 3.6 31.6 - - + +
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Residues in contact with LYS 631 (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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627A LEU* 3.0 31.8 + - + +
628A GLY* 3.9 6.7 - - - +
629A VAL 3.2 0.4 - - - -
630A LEU* 1.3 75.6 - - - +
632A GLN* 1.3 68.4 + - - +
633A GLN* 3.3 15.9 + - - +
651A VAL* 2.7 37.7 + - + +
652A GLN* 3.4 15.4 + - - +
654A MET 2.6 28.9 + - - -
655A GLY* 5.2 0.2 - - - -
656A PHE* 4.1 20.2 - - + +
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Residues in contact with GLN 632 (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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628A GLY 3.3 10.0 + - - +
629A VAL* 3.2 17.5 + - - +
630A LEU 4.6 2.8 - - - +
631A LYS* 1.3 78.8 - - - +
633A GLN* 1.3 74.2 + - - +
634A PRO 3.5 14.5 + - - +
635A PRO* 3.3 13.7 - - - +
636A ALA* 3.4 32.5 - - - +
755A PRO* 4.2 5.9 - - - +
758A ARG* 2.9 46.6 + - + +
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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