Contacts of the helix formed by residues 638 - 643 (chain A) in PDB entry 4AY6
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 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A CYS* 3.9 18.4 - - - -
628A ASN* 3.1 29.1 + - - +
630A ASN* 5.1 0.7 - - - +
631A GLY* 3.1 30.7 + - - +
632A TYR* 3.9 21.6 - - - -
636A ALA* 4.0 5.7 - - - +
637A ARG* 1.3 74.1 + - - +
639A GLU* 1.3 61.2 + - - +
640A LEU 2.9 1.3 - - - -
641A PHE* 2.7 28.9 + - - +
642A ALA* 2.8 12.0 + - - +
663A PHE* 4.1 15.4 - - + -
1398E GLN* 4.7 4.4 + - - +
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Residues in contact with GLU 639 (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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521A CYS* 4.0 26.8 - - + +
524A LYS* 3.3 35.5 + - + +
525A ILE* 3.6 22.6 - - + +
611A ASN* 3.1 32.6 + - - +
636A ALA 5.1 0.3 - - - +
637A ARG* 3.5 9.4 - - - -
638A ASN* 1.3 81.6 + - - +
640A LEU* 1.3 63.3 + - - +
642A ALA* 3.1 3.6 + - - +
643A LEU* 3.1 27.3 + - - +
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Residues in contact with LEU 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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551A VAL* 4.4 10.3 - - + -
583A LEU* 4.0 17.7 - - + -
605A LEU* 4.0 23.6 - - + -
611A ASN* 3.8 19.5 - - - +
614A ALA* 3.5 30.5 - - + -
615A ALA* 3.8 8.1 - - - +
618A ILE* 4.6 11.4 - - + -
626A LEU* 5.5 2.7 - - + -
637A ARG* 3.2 28.9 + - + +
638A ASN 2.9 0.6 - - - -
639A GLU* 1.3 79.4 - - - +
641A PHE* 1.3 68.3 + - + +
643A LEU* 3.2 17.5 + - - +
645A PRO* 3.6 14.1 - - - +
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Residues in contact with PHE 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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551A VAL* 3.9 28.3 - - + -
626A LEU* 3.6 32.5 - - + -
627A VAL 3.8 6.5 - - - -
628A ASN* 3.2 57.0 - - + +
637A ARG 4.3 4.9 - - - -
638A ASN* 2.7 24.1 + - - +
640A LEU* 1.3 79.2 - - + +
642A ALA* 1.3 55.5 + - - +
644A ARG* 2.8 18.9 + - - -
645A PRO* 4.8 0.7 - - - -
649A GLN* 3.1 30.2 + - + +
663A PHE* 3.6 24.8 - - + +
664A MET* 3.8 14.6 - - + -
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Residues in contact with ALA 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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521A CYS* 4.4 7.0 - - + -
522A LEU* 4.7 10.3 - - + +
525A ILE* 4.2 23.9 - - + +
638A ASN 2.8 8.8 + - - +
639A GLU* 3.1 13.9 + - - +
641A PHE* 1.3 77.6 - - - +
643A LEU* 1.3 60.5 - - - +
644A ARG* 3.2 7.2 + - - +
663A PHE* 3.5 37.4 - - + +
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Residues in contact with LEU 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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525A ILE* 3.9 36.6 - - + +
528A LEU* 4.8 4.5 - - + -
530A LYS* 4.1 30.7 - - + -
532A PRO* 5.7 1.6 - - - +
533A TYR* 3.4 17.6 + - + -
611A ASN* 3.4 32.5 - - + +
612A GLY* 4.3 4.0 - - - +
615A ALA* 3.6 18.4 - - + -
639A GLU 3.1 19.9 + - - +
640A LEU* 3.5 6.7 - - - +
641A PHE 3.1 0.6 - - - -
642A ALA* 1.3 74.5 - - - +
644A ARG* 1.3 72.0 + - - +
645A PRO 3.6 0.9 - - - -
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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