Contacts of the helix formed by residues 639 - 651 (chain A) in PDB entry 3ZRH
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 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638A GLY* 1.3 81.8 - - - +
640A GLU* 1.3 70.2 + - - +
641A GLU* 2.7 33.2 + - + +
642A GLN* 3.6 11.7 - - + +
643A GLN* 3.0 23.1 + - - -
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Residues in contact with GLU 640 (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 LEU* 4.1 14.1 - - + +
639A ASN* 1.3 81.1 - - - +
641A GLU* 1.3 66.6 + - - +
643A GLN* 3.8 7.1 - - - +
644A GLU* 3.1 28.0 + - - +
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Residues in contact with GLU 641 (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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639A ASN* 2.7 21.3 + - + +
640A GLU* 1.3 79.5 - - - +
642A GLN* 1.3 56.7 + - + +
644A GLU* 3.8 8.5 + - - +
645A LYS* 3.2 23.4 + - - +
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Residues in contact with GLN 642 (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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636A GLU* 3.0 29.0 + - - +
637A LEU 3.4 15.5 - - - +
638A GLY* 3.5 5.0 + - - -
639A ASN* 3.2 18.0 + - + +
640A GLU 3.1 0.4 - - - -
641A GLU* 1.3 79.3 - - + +
643A GLN* 1.3 72.6 + - - +
645A LYS* 3.1 9.0 + - + +
646A LEU* 3.0 35.5 + - - +
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Residues in contact with GLN 643 (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 LEU* 3.6 22.9 - - + -
627A LEU 5.6 1.3 - - - +
628A HIS* 6.5 0.2 - - - -
629A VAL* 4.6 19.7 - - + +
632A LEU* 3.2 27.4 - - - +
636A GLU 3.8 2.3 - - - +
637A LEU* 4.1 2.2 - - - +
638A GLY 2.8 33.7 + - - +
639A ASN 3.0 11.1 + - - +
640A GLU* 3.8 3.0 - - - +
642A GLN* 1.3 85.9 + - - +
644A GLU* 1.3 66.8 + - - +
646A LEU* 3.1 9.8 + - + +
647A LEU* 2.9 25.7 + - - +
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Residues in contact with GLU 644 (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 LEU* 3.9 8.4 - - + +
640A GLU 3.1 16.7 + - - +
641A GLU* 3.9 6.7 - - - +
643A GLN* 1.3 78.7 - - - +
645A LYS* 1.3 64.6 + - - +
647A LEU* 3.1 13.9 + - - +
648A ARG* 2.7 60.8 + - + +
655A VAL* 5.3 0.5 - - - +
661A LEU* 4.3 24.1 - - + +
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Residues in contact with LYS 645 (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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641A GLU 3.2 12.4 + - - +
642A GLN* 3.1 15.3 + - + +
644A GLU* 1.3 79.6 - - - +
646A LEU* 1.3 62.5 + - - +
648A ARG* 3.2 12.1 + - - +
649A GLU* 3.1 28.0 + - - +
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Residues in contact with LEU 646 (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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563A LEU* 3.8 28.3 - - + -
565A LEU* 4.7 3.6 - - + -
569A GLN* 5.2 0.2 - - - +
629A VAL* 4.3 8.1 - - + -
632A LEU* 4.1 30.1 - - + -
636A GLU* 5.0 12.6 - - + +
642A GLN* 3.0 26.3 + - - +
643A GLN* 3.2 12.8 - - - +
645A LYS* 1.3 73.9 - - - +
647A LEU* 1.3 65.8 + - - +
649A GLU* 3.0 27.2 + - - +
650A TRP* 3.3 41.2 - - + +
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Residues in contact with LEU 647 (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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561A VAL* 4.0 19.1 - - + -
563A LEU* 4.6 7.2 - - + -
619A LEU* 4.6 18.8 - - + +
626A LEU* 4.0 35.2 - - + -
627A LEU* 4.9 2.9 - - + +
629A VAL* 3.7 30.7 - - + -
643A GLN 2.9 17.8 + - - +
644A GLU* 3.1 9.6 + - + +
646A LEU* 1.3 75.4 - - - +
648A ARG* 1.3 56.7 + - + +
650A TRP* 3.2 2.9 + - - +
651A LEU* 2.8 59.5 + - + +
653A CYS* 4.2 3.6 - - - -
661A LEU* 5.0 1.6 - - + -
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Residues in contact with ARG 648 (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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644A GLU* 2.7 48.7 + - + +
645A LYS* 3.5 12.6 - - - +
646A LEU 3.1 0.2 - - - -
647A LEU* 1.3 76.5 - - - +
649A GLU* 1.3 61.5 + - - +
651A LEU 3.1 18.1 - - - +
653A CYS* 4.1 34.7 + - + +
654A CYS* 4.8 3.2 - - - +
655A VAL* 3.8 15.6 - - - +
661A LEU* 3.8 17.9 - - + +
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Residues in contact with GLU 649 (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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569A GLN* 3.2 35.5 + - - +
574A LYS* 3.1 24.3 + - - -
645A LYS* 3.1 16.4 + - - +
646A LEU* 3.0 25.3 + - - +
648A ARG* 1.3 78.2 - - - +
650A TRP* 1.3 61.5 + - + +
651A LEU 4.5 0.2 - - - +
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Residues in contact with TRP 650 (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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536A PRO* 3.8 9.3 - - + +
563A LEU* 3.9 30.3 - - + -
564A PRO* 3.5 49.4 - - + -
565A LEU* 3.9 28.3 - - + +
567A TRP 3.6 15.9 - - - -
569A GLN* 3.2 53.1 - - + +
572A CYS* 4.2 11.2 - - + -
573A TRP 4.5 1.0 - - - +
574A LYS* 3.8 24.5 - - - +
646A LEU* 3.3 41.7 + - + +
647A LEU 3.2 3.6 + - - +
649A GLU* 1.3 79.6 - - + +
651A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 651 (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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536A PRO* 3.4 33.9 - - + -
538A ILE* 4.9 1.8 - - + -
561A VAL* 4.5 8.5 - - + -
563A LEU* 4.6 2.0 - - + -
574A LYS* 3.6 19.6 - - - +
576A PRO* 4.0 17.9 - - + -
619A LEU* 4.0 23.3 - - + -
647A LEU* 2.8 42.1 + - + +
648A ARG 3.1 21.0 - - - +
649A GLU 4.4 0.3 - - - -
650A TRP* 1.3 82.9 - - + +
652A ASP* 1.3 61.1 + - - +
653A CYS* 3.6 13.5 + - - -
663A ALA* 4.2 8.5 - - + -
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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