Contacts of the helix formed by residues 638 - 643 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D CYS* 3.9 18.5 - - - -
628D ASN* 3.1 28.8 + - - +
630D ASN* 5.1 0.5 - - - +
631D GLY* 3.1 31.5 + - - +
632D TYR* 3.8 22.4 - - + -
636D ALA* 4.0 6.0 - - - +
637D ARG* 1.3 73.4 + - - +
639D GLU* 1.3 69.8 + - - +
640D LEU 3.0 2.2 - - - -
641D PHE* 2.8 20.5 + - - +
642D ALA* 2.9 12.6 + - - +
663D PHE* 4.2 14.4 - - + -
1398H GLN* 4.6 4.2 + - - +
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Residues in contact with GLU 639 (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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521D CYS* 4.0 22.7 - - + +
524D LYS* 3.3 34.7 + - + +
525D ILE* 3.6 19.1 - - + +
611D ASN* 3.1 31.9 + - - +
636D ALA 5.1 0.3 - - - +
637D ARG* 3.5 8.4 - - - -
638D ASN* 1.3 83.7 + - - +
640D LEU* 1.3 60.6 + - - +
642D ALA* 3.3 10.6 + - - +
643D LEU* 3.1 29.2 + - - +
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Residues in contact with LEU 640 (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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551D VAL* 4.3 11.4 - - + -
583D LEU* 4.0 26.5 - - + -
605D LEU* 4.1 12.8 - - + -
611D ASN* 3.9 14.4 - - - +
614D ALA* 3.5 31.4 - - + -
615D ALA* 3.8 13.4 - - - +
618D ILE* 4.4 10.8 - - + -
626D LEU* 5.4 2.0 - - + -
637D ARG* 3.3 29.8 + - + +
639D GLU* 1.3 78.4 - - - +
641D PHE* 1.3 68.2 + - + +
643D LEU* 3.2 16.5 + - - +
645D PRO* 3.5 20.4 - - - +
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Residues in contact with PHE 641 (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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551D VAL* 4.0 27.8 - - + -
626D LEU* 3.7 30.1 - - + -
627D VAL 3.7 6.5 - - - -
628D ASN* 3.2 59.9 - - + +
637D ARG 4.4 2.2 - - - -
638D ASN* 2.8 19.1 + - - +
640D LEU* 1.3 80.1 - - + +
642D ALA* 1.3 61.0 + - - +
643D LEU 3.1 2.0 - - - -
644D ARG* 2.8 18.5 + - - -
645D PRO* 4.7 0.4 - - - -
649D GLN* 3.0 30.9 + - + +
663D PHE* 3.6 24.3 - - + +
664D MET* 3.7 15.3 - - + -
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Residues in contact with ALA 642 (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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521D CYS* 4.4 7.2 - - + -
522D LEU* 4.8 9.3 - - + +
525D ILE* 4.3 23.1 - - + +
638D ASN 2.9 9.5 + - - +
639D GLU* 3.3 15.0 + - - +
641D PHE* 1.3 76.4 - - - +
643D LEU* 1.3 59.5 + - - +
644D ARG* 3.2 6.1 + - - +
663D PHE* 3.4 37.8 - - + +
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Residues in contact with LEU 643 (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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525D ILE* 3.9 36.3 - - + +
528D LEU* 4.8 3.6 - - + -
530D LYS* 4.0 31.4 - - + -
532D PRO* 5.7 1.9 - - - +
533D TYR* 3.5 16.1 + - + -
611D ASN* 3.3 33.9 - - + +
612D GLY* 4.4 4.0 - - - -
615D ALA* 3.5 19.5 - - + -
639D GLU 3.1 18.4 + - - +
640D LEU* 3.5 7.6 - - - +
641D PHE 3.1 0.6 - - - -
642D ALA* 1.3 74.5 - - - +
644D ARG* 1.3 73.3 + - - +
645D PRO 3.7 0.4 - - - -
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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