Contacts of the helix formed by residues 634 - 642 (chain D) in PDB entry 6PUO
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 ARG 634 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492D LEU 4.6 0.8 + - - -
493D ILE 3.3 19.7 + - - -
495D ASN* 3.4 53.4 - - - +
525D ASN 5.5 2.6 + - - -
527D ASP* 4.4 24.0 + - - +
628D TRP* 4.5 11.6 - - - -
629D ALA* 3.5 15.9 + - + +
630D ILE* 5.2 0.6 - - - +
632D GLN* 2.8 42.2 + - + +
633D ASN* 1.3 78.5 - - - +
635D ARG* 1.3 64.9 + - - +
636D GLU 3.6 1.8 - - - -
637D LEU* 4.0 24.8 - - + +
638D ALA* 3.4 22.2 + - - +
678D LEU* 5.3 1.9 - - - +
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Residues in contact with ARG 635 (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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633D ASN* 3.9 5.6 + - - +
634D ARG* 1.3 73.6 - - - +
636D GLU* 1.3 61.5 + - - +
638D ALA* 3.2 4.7 + - - +
639D GLY* 3.0 25.8 + - - -
678D LEU* 3.7 36.1 - - + +
681D GLU* 3.1 34.9 + - - +
682D TYR* 5.0 0.5 + - - -
685D ARG* 5.4 1.1 - - - +
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Residues in contact with GLU 636 (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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495D ASN* 6.1 1.1 - - - +
497D PRO* 4.2 24.5 - - + -
634D ARG 3.6 0.2 - - - -
635D ARG* 1.3 79.9 - - - +
637D LEU* 1.3 61.7 + - - +
639D GLY* 3.8 1.8 + - - +
640D ILE* 3.3 29.9 + - + +
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Residues in contact with LEU 637 (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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491D ALA 5.8 0.2 - - - +
492D LEU* 4.0 32.1 - - + +
495D ASN* 4.3 15.4 + - - +
496D LYS 5.4 0.2 - - - -
497D PRO* 4.3 15.0 - - + -
500D VAL* 4.0 32.1 - - + -
628D TRP* 4.6 9.9 - - + -
629D ALA* 4.5 8.5 - - + -
634D ARG* 3.8 33.9 + - + +
635D ARG 3.2 0.6 - - - -
636D GLU* 1.3 77.7 - - - +
638D ALA* 1.3 60.2 + - - +
640D ILE* 3.1 8.5 + - + +
641D ILE* 2.9 40.1 + - + +
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Residues in contact with ALA 638 (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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626D LEU* 4.1 14.6 - - + +
629D ALA* 4.5 8.2 - - + +
630D ILE* 3.7 24.2 - - + -
634D ARG 3.4 15.4 + - - +
635D ARG* 3.2 5.9 + - - +
637D LEU* 1.3 77.8 - - - +
639D GLY* 1.3 57.9 + - - +
641D ILE* 4.4 1.3 - - - +
642D TRP* 3.0 28.8 + - - +
678D LEU* 5.7 0.4 - - + -
682D TYR* 3.2 23.6 + - + +
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Residues in contact with GLY 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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635D ARG 3.0 15.2 + - - -
636D GLU* 3.8 2.7 + - - -
637D LEU 3.2 0.2 - - - -
638D ALA* 1.3 78.3 - - - +
640D ILE* 1.3 60.7 + - - +
642D TRP* 4.7 1.9 - - - +
643D ALA* 4.0 15.1 + - - +
682D TYR* 3.6 6.9 + - - -
685D ARG* 4.1 25.0 + - - -
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Residues in contact with ILE 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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497D PRO* 4.4 14.1 - - + +
500D VAL* 5.1 7.4 - - + -
501D LYS* 3.7 36.6 - - + +
504D LEU* 4.0 27.1 - - + -
510D LEU* 6.1 1.1 - - + -
636D GLU* 3.3 19.7 + - + +
637D LEU* 3.1 13.1 + - + +
639D GLY* 1.3 77.9 - - - +
641D ILE* 1.3 69.9 + - + +
643D ALA* 3.2 18.4 + - - +
644D GLN* 4.0 10.3 + - - +
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Residues in contact with ILE 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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492D LEU* 5.6 4.9 - - + -
500D VAL* 6.4 2.0 - - + -
510D LEU* 5.0 14.1 - - + +
622D ILE* 4.1 24.5 - - + +
625D LEU* 3.8 41.1 - - + +
626D LEU* 4.1 28.3 - - + +
628D TRP* 5.9 0.9 - - + -
629D ALA* 4.2 12.8 - - + -
637D LEU* 2.9 31.2 + - + +
638D ALA 4.1 2.2 - - - +
640D ILE* 1.3 81.2 - - + +
642D TRP* 1.3 63.2 + - - +
644D GLN* 3.2 14.3 + - - +
645D SER* 3.7 6.1 + - - -
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Residues in contact with TRP 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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626D LEU* 4.0 25.7 - - + +
638D ALA 3.0 17.1 + - - +
639D GLY* 4.7 2.5 - - - +
641D ILE* 1.3 76.9 - - - +
643D ALA* 1.3 68.3 + - + +
645D SER* 3.1 20.8 + - - -
648D CYS* 3.3 44.9 + - + +
651D ALA* 4.3 7.2 - - + -
652D ALA* 4.1 12.7 - - + +
682D TYR* 4.2 19.5 - + + +
685D ARG* 3.6 49.4 - - + -
686D ALA* 5.8 0.4 - - - -
689D VAL* 3.9 25.6 - - + -
1129D LYS* 4.5 12.7 + - + +
1132D TYR* 4.7 3.1 - + - -
1133D LEU* 4.4 19.3 - - + -
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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