Contacts of the helix formed by residues 633 - 645 (chain D) in PDB entry 5JA4
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 SER 633 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603D HIS* 3.6 4.9 - - - -
627D ARG* 3.9 14.1 - - - +
632D LEU* 1.3 76.3 - - - +
634D PRO* 1.4 69.8 - - - +
635D LEU* 4.0 6.0 + - - +
636D GLU* 3.1 31.1 + - - +
637D THR* 2.8 28.4 + - - -
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Residues in contact with PRO 634 (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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600D THR* 6.0 0.2 - - + -
602D LEU* 4.2 21.8 - - + -
603D HIS* 3.3 30.3 - - + +
606D LEU* 3.4 13.3 - - + +
623D SER 5.6 0.2 - - - -
624D VAL* 3.5 28.9 - - - +
625D THR 5.2 0.2 - - - -
626D LEU* 4.6 3.4 - - + +
627D ARG 3.5 17.7 - - - +
633D SER* 1.4 88.1 - - - +
635D LEU* 1.3 62.1 + - - +
637D THR* 3.4 4.4 + - - -
638D LEU 3.1 17.0 + - - -
664D LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 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 SER* 3.3 5.9 + - - +
634D PRO* 1.3 74.9 - - - +
636D GLU* 1.3 57.0 + - + +
638D LEU* 3.1 4.7 + - + +
639D GLN* 2.7 74.3 + - + +
661D GLU* 3.7 35.2 - - + +
664D LEU* 3.6 23.5 - - + +
665D GLN* 3.7 32.3 - - + +
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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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631D GLY 4.1 4.0 - - - +
632D LEU* 3.5 17.0 - - + -
633D SER* 3.1 39.1 + - - +
635D LEU* 1.3 79.2 - - + +
637D THR* 1.3 52.3 + - - +
639D GLN* 3.4 17.7 + - - +
640D GLN* 2.8 36.3 + - - +
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Residues in contact with THR 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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603D HIS* 3.0 50.6 + - - +
606D LEU* 4.0 9.9 - - + -
607D ASN* 3.3 28.2 - - - +
632D LEU* 4.3 9.4 - - - +
633D SER 2.8 7.8 + - - -
634D PRO* 3.4 10.5 - - - -
636D GLU* 1.3 72.6 - - - +
638D LEU* 1.3 60.5 + - - +
640D GLN* 3.2 6.0 + - - +
641D TRP* 2.9 27.4 + - - +
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Residues in contact with LEU 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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606D LEU* 4.1 18.2 - - + +
611D PHE* 3.8 25.6 - - + -
634D PRO 3.1 8.7 + - - +
635D LEU* 3.1 7.9 + - + +
637D THR* 1.3 79.3 - - - +
639D GLN* 1.3 53.4 + - - +
641D TRP* 2.9 14.2 + - + +
642D VAL* 2.7 49.4 + - + +
657D ALA* 3.8 7.6 - - + +
660D MET* 3.5 31.2 - - + -
661D GLU* 3.7 31.4 - - - +
664D LEU* 4.0 6.5 - - + -
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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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635D LEU* 2.7 51.0 + - + +
636D GLU* 3.6 23.9 - - - +
638D LEU* 1.3 73.0 - - - +
640D GLN* 1.3 57.6 + - - +
642D VAL* 3.4 5.3 + - - +
643D LYS* 2.9 30.4 + - - +
661D GLU* 3.2 33.0 + - - +
665D GLN* 4.3 7.1 + - - -
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Residues in contact with GLN 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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636D GLU 2.8 21.8 + - - +
637D THR* 3.8 6.1 - - - +
639D GLN* 1.3 73.4 - - - +
641D TRP* 1.3 61.6 + - - +
643D LYS* 3.8 8.6 - - - +
644D LEU* 3.2 26.0 + - - +
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Residues in contact with TRP 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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13B GLY* 3.4 33.0 - - - -
14B GLY 2.9 21.2 + - - -
606D LEU 3.4 16.4 - - - +
607D ASN* 3.0 25.5 + - - +
608D CYS 4.6 0.2 - - - -
609D GLY* 3.5 19.8 - - - +
611D PHE* 3.6 32.1 - + - -
637D THR 2.9 13.8 + - - +
638D LEU* 2.9 17.0 + - + +
640D GLN* 1.3 75.5 - - - +
642D VAL* 1.3 88.3 + - + +
644D LEU* 3.2 3.5 + - - +
645D TYR* 3.0 48.7 + + - -
649D LEU* 4.0 25.4 - - + -
653D THR* 4.2 3.8 - - + -
657D ALA* 4.7 0.7 - - + -
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Residues in contact with VAL 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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638D LEU* 2.7 41.4 + - + +
639D GLN* 3.6 6.5 - - - +
641D TRP* 1.3 84.6 - - + +
643D LYS* 1.3 53.9 + - - +
645D TYR* 3.1 1.8 + - - -
646D ARG* 2.7 45.2 + - + -
649D LEU* 4.9 12.1 - - + +
657D ALA* 4.1 16.8 - - + -
661D GLU* 4.4 9.4 - - - +
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Residues in contact with LYS 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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639D GLN 2.9 21.0 + - - +
640D GLN* 3.8 10.3 - - - +
642D VAL* 1.3 76.1 - - - +
644D LEU* 1.3 66.4 + - + +
646D ARG* 3.5 19.8 + - + +
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Residues in contact with LEU 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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640D GLN 3.2 16.1 + - - +
641D TRP* 3.6 3.4 - - - +
643D LYS* 1.3 84.0 - - + +
645D TYR* 1.3 103.7 + - + +
646D ARG 3.8 0.2 + - - -
648D ASP* 5.5 0.9 - - - +
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Residues in contact with TYR 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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12B LYS 5.5 0.7 - - - -
13B GLY* 4.3 4.0 - - - -
14B GLY* 3.3 36.2 - - - -
15B ALA* 3.4 9.9 + - - -
607D ASN 5.0 0.2 - - - -
641D TRP* 3.0 62.7 + + + +
642D VAL* 3.3 2.9 - - - +
644D LEU* 1.3 102.6 - - + +
646D ARG* 1.3 58.0 + - - +
647D ARG 2.4 25.0 - - - +
648D ASP* 5.0 10.8 - - + -
649D LEU* 3.3 29.7 + - + +
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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