Contacts of the helix formed by residues 636 - 646 (chain D) in PDB entry 1K0Y
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 636 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ARG* 4.8 3.0 + - - -
140A TYR 4.1 8.5 - - - +
141A ARG* 3.9 23.3 - - + -
632D LEU 3.4 12.8 - - - +
633D VAL 3.6 13.7 - - - +
634D VAL 3.4 8.1 - - - +
635D TYR* 1.3 87.4 - - - +
637D TRP* 1.4 66.7 + - + +
638D THR 3.1 0.2 - - - -
639D GLN* 3.0 41.4 + - - +
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Residues in contact with TRP 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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88A ALA 5.1 2.7 - - - +
92A ARG* 3.5 47.4 - - + +
94A ASP* 3.1 35.9 + - + -
95A PRO* 3.8 9.9 - - + +
140A TYR* 3.4 33.8 + + + +
141A ARG* 4.1 5.4 - - + -
635D TYR* 3.4 41.7 - + + -
636D PRO* 1.4 88.0 - - + +
638D THR* 1.4 67.1 + - + +
639D GLN 3.1 1.5 + - - -
640D ARG* 3.2 19.2 + - - +
702D ASN* 5.1 2.7 - - - -
705D LEU* 4.0 10.2 - - + +
802D CNO 3.5 53.8 - + + -
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Residues in contact with THR 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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631D LEU* 3.4 27.0 + - + +
632D LEU* 3.4 19.5 - - - +
635D TYR* 2.7 33.5 + - + +
637D TRP* 1.4 75.8 - - + +
639D GLN* 1.4 59.4 + - - +
640D ARG 3.1 7.4 + - - -
641D PHE* 3.5 13.6 + - - -
642D PHE* 3.4 19.6 - - - -
702D ASN* 3.3 26.9 - - - +
705D LEU* 4.2 10.8 - - + -
748D HEM 4.3 2.2 - - - -
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Residues in contact with GLN 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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92A ARG* 3.9 17.5 + - - +
632D LEU* 2.8 44.0 + - + +
633D VAL* 4.9 0.8 - - - +
636D PRO* 3.0 27.6 + - - +
638D THR* 1.4 73.1 + - - +
640D ARG* 1.4 55.1 + - - +
641D PHE 3.1 5.6 - - - -
642D PHE* 2.9 34.5 + - - +
643D GLU* 3.8 2.8 + - - +
648D LEU* 3.6 42.5 + - + +
654D VAL* 4.8 2.8 - - - +
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Residues in contact with ARG 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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41A THR 5.1 3.4 + - - -
42A TYR* 3.7 33.3 + - - +
90A LYS 5.3 1.0 + - - +
91A LEU* 3.0 28.4 + - - +
92A ARG* 3.2 49.0 + - + +
143A HEM 6.0 2.0 - - - +
637D TRP* 3.2 14.5 + - - +
638D THR 3.1 0.6 - - - -
639D GLN* 1.4 75.8 - - - +
641D PHE* 1.4 103.3 - - + +
642D PHE 3.3 1.6 + - - -
643D GLU* 4.1 13.5 - - - +
697D HIS 4.7 3.8 + - - -
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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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42A TYR* 5.5 1.8 - + - -
638D THR* 3.6 13.9 - - - -
639D GLN 3.1 1.4 - - - -
640D ARG* 1.4 114.5 - - + +
642D PHE* 1.4 74.6 + - + +
643D GLU 3.9 1.5 + - - -
645D PHE* 5.7 0.3 - - - -
696D LEU 4.3 6.5 - - - -
697D HIS 3.4 21.5 - - - -
698D VAL* 3.8 22.2 - - + -
699D ASP* 4.1 4.3 - - + -
702D ASN* 3.2 35.7 - - - -
748D HEM 3.6 43.7 - - + +
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Residues in contact with PHE 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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628D LEU* 4.4 8.7 - - + -
632D LEU* 3.9 24.2 - - + -
638D THR 3.4 23.1 - - - -
639D GLN* 2.9 12.7 + - - +
641D PHE* 1.4 85.7 - - + +
643D GLU* 1.4 62.9 + - - +
644D SER* 3.1 4.7 - - - +
645D PHE* 3.0 56.8 + + + +
646D GLY 4.7 0.2 + - - -
648D LEU* 3.9 16.0 - - + +
663D HIS* 3.6 31.0 - + - -
748D HEM 3.7 50.5 - + + -
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Residues in contact with GLU 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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92A ARG* 2.8 41.6 + - - -
639D GLN 3.8 1.7 + - - -
640D ARG* 4.1 14.2 - - - +
641D PHE 3.9 1.4 - - - -
642D PHE* 1.4 73.7 - - - +
644D SER* 1.4 58.0 + - - +
645D PHE 3.3 0.7 + - - -
646D GLY 4.3 7.8 + - - +
648D LEU* 5.7 1.3 - - - -
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Residues in contact with SER 644 (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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642D PHE* 4.9 1.4 - - - -
643D GLU* 1.4 75.7 - - - +
645D PHE* 1.4 73.6 + - - +
646D GLY 3.3 2.8 + - - -
659D LYS* 3.5 19.8 + - - +
748D HEM 5.0 5.0 + - - -
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Residues in contact with PHE 645 (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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628D LEU* 4.8 2.0 - - + -
632D LEU* 5.5 0.2 - - + -
641D PHE 5.7 0.4 - - - -
642D PHE* 3.0 53.9 + + + +
644D SER* 1.4 90.9 - - - +
646D GLY* 1.3 58.6 + - - +
648D LEU* 4.6 7.4 - - + -
657D ASN* 2.7 30.9 + - - +
659D LYS* 3.5 41.9 - - + +
660D VAL* 3.9 26.5 - - + -
663D HIS* 3.8 27.6 - + + -
748D HEM 4.4 17.5 - - + -
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Residues in contact with GLY 646 (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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642D PHE 4.7 0.4 + - - +
643D GLU 4.3 7.1 + - - +
644D SER 3.3 4.8 + - - -
645D PHE* 1.3 80.3 - - - +
647D ASP* 1.4 63.3 + - - -
648D LEU* 3.4 10.7 + - - +
657D ASN* 4.1 0.2 - - - -
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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