Contacts of the helix formed by residues 633 - 647 (chain A) in PDB entry 3L4U
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 LEU 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A PHE* 4.9 2.2 - - + -
629A ILE* 3.1 33.6 + - + +
630A ARG 3.1 5.3 + - - +
632A THR* 1.3 74.5 - - - +
634A LEU* 1.3 64.5 + - - +
635A PRO* 3.3 4.3 - - - -
636A TYR* 3.0 14.6 + - + +
637A LEU* 3.0 19.4 + - - +
674A TRP* 3.9 14.4 - - + -
678A LEU* 4.2 27.1 - - + -
703A TYR* 4.1 24.7 - - + +
729A LEU* 5.5 2.5 - - + -
735A PHE* 4.5 19.3 - - + -
736A PRO 4.5 4.7 - - - +
737A THR* 4.0 22.0 - - + -
755A ILE* 4.9 0.9 - - + -
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Residues in contact with LEU 634 (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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289A TYR* 3.4 22.2 - - + +
292A LEU* 3.8 40.2 - - + +
630A ARG* 3.1 25.9 + - + +
631A TYR* 3.0 32.2 + - + +
633A LEU* 1.3 78.4 - - - +
635A PRO* 1.4 58.3 - - + +
637A LEU* 3.8 17.6 - - + +
638A TYR* 2.8 31.5 + - - +
744A THR* 3.6 31.2 - - + -
747A SER* 5.0 2.9 - - - +
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Residues in contact with PRO 635 (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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289A TYR* 3.6 14.1 - - - +
631A TYR 4.2 0.4 - - - +
632A THR 3.5 12.8 - - - +
633A LEU 3.4 4.5 - - - -
634A LEU* 1.4 89.0 - - + +
636A TYR* 1.3 56.7 + - - +
638A TYR* 3.8 5.3 - - + +
639A THR* 2.8 32.9 + - - -
736A PRO* 3.8 13.0 - - + +
737A THR 3.8 7.6 - - - +
738A GLN* 3.7 28.9 - - + +
752A LEU* 4.7 2.9 - - + -
768A LEU* 3.7 23.2 - - + +
770A TRP* 4.4 10.1 - - + -
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Residues in contact with TYR 636 (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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633A LEU* 3.0 19.4 + - + +
635A PRO* 1.3 76.7 - - - +
637A LEU* 1.3 66.8 + - - +
639A THR* 3.2 8.1 + - - -
640A LEU* 3.0 46.7 + - + +
674A TRP* 2.7 48.9 + + + -
676A PRO* 3.4 12.2 - - + +
677A GLY* 3.2 19.6 + - - -
678A LEU* 4.3 7.6 - - + -
733A TYR* 6.5 0.9 - + - -
734A ILE 5.1 3.6 - - - -
735A PHE* 3.8 32.5 - + + -
736A PRO* 3.5 32.8 + - + +
767A GLU 5.7 0.9 - - - -
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.9 15.5 - - + -
595A PRO* 4.7 5.8 - - + +
630A ARG* 4.0 19.1 - - - +
633A LEU 3.0 8.8 + - - +
634A LEU* 3.8 18.2 - - + +
636A TYR* 1.3 76.3 - - - +
638A TYR* 1.3 57.9 + - - +
640A LEU* 3.1 13.9 + - + +
641A PHE* 2.9 45.3 + - + -
651A VAL* 3.6 31.2 - - + -
674A TRP* 3.7 50.3 - - + +
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Residues in contact with TYR 638 (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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286A LEU* 4.0 11.5 - - + +
287A PRO* 3.7 19.5 - - + -
289A TYR* 3.5 41.5 - + + -
292A LEU* 3.8 18.3 - - + +
520A ARG* 2.7 22.7 + - - -
634A LEU 2.8 21.3 + - - +
635A PRO 3.8 4.0 - - - +
637A LEU* 1.3 68.7 - - - +
639A THR* 1.3 61.2 + - - +
641A PHE* 3.1 8.3 + - + +
642A PHE* 2.8 27.0 + - - +
748A ARG* 4.8 3.4 - - - -
769A PHE* 3.7 34.3 - + - -
770A TRP* 5.1 4.0 - + - -
771A ASP* 2.5 35.8 + - - -
773A GLY* 3.4 5.4 - - - -
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Residues in contact with THR 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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635A PRO 2.8 21.6 + - - -
636A TYR* 3.7 8.5 - - + -
638A TYR* 1.3 76.3 - - - +
640A LEU* 1.3 59.0 + - + +
642A PHE* 3.2 6.4 + - + +
643A ARG* 2.9 27.0 + - - +
767A GLU* 3.7 39.4 + - + +
768A LEU* 3.7 7.5 - - - +
769A PHE* 3.0 44.3 + - + +
786A LEU* 5.0 0.2 - - + -
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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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636A TYR* 3.0 37.3 + - + +
637A LEU* 3.1 14.3 + - + +
639A THR* 1.3 78.8 - - + +
641A PHE* 1.3 58.3 + - - +
643A ARG* 3.2 11.0 + - + +
644A ALA* 2.9 27.2 + - - +
650A THR 4.9 2.7 - - - +
651A VAL* 3.8 24.6 - - + +
653A ARG* 5.0 5.2 - - - +
674A TRP* 3.6 17.5 - - + -
675A GLY* 3.4 40.8 - - - +
676A PRO* 4.1 11.2 - - + -
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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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285A ALA 5.3 2.1 - - - +
286A LEU* 3.7 4.9 - - + +
287A PRO* 3.5 34.3 - - + -
292A LEU* 3.5 25.8 - - + -
566A PRO* 3.9 17.5 - - + -
567A MET* 3.8 35.4 - - + -
595A PRO* 4.0 22.9 - - + -
637A LEU* 2.9 48.3 + - + -
638A TYR* 3.1 8.9 + - + +
640A LEU* 1.3 73.4 - - - +
642A PHE* 1.3 59.9 + - - +
644A ALA* 3.3 2.8 + - + +
645A HIS* 2.9 31.2 + - - +
651A VAL* 4.0 14.4 - - + -
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Residues in contact with PHE 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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286A LEU* 3.6 9.5 - - - +
638A TYR 2.8 9.2 + - - +
639A THR* 3.2 11.9 + - + +
641A PHE* 1.3 75.9 - - - +
643A ARG* 1.3 87.7 + - - +
645A HIS* 3.3 2.2 + - - +
646A SER* 2.8 53.9 + - - -
769A PHE* 3.4 61.5 - + + -
779A VAL* 3.8 21.5 - - + -
784A TYR* 4.1 18.6 - + - -
786A LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 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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639A THR 2.9 18.3 + - - +
640A LEU* 3.7 12.8 - - + +
642A PHE* 1.3 98.5 - - + +
644A ALA* 1.3 60.9 + - - +
646A SER* 3.7 6.8 + - - -
647A ARG* 2.8 69.1 + - - +
648A GLY 2.9 6.1 + - - -
649A ASP* 3.5 22.2 + - + +
767A GLU* 2.6 45.0 + - - +
786A LEU* 4.0 11.9 - - - +
788A GLU* 4.0 8.7 + - - -
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Residues in contact with ALA 644 (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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283A ARG* 3.7 1.4 - - - -
284A PRO* 3.5 28.8 - - + +
566A PRO* 4.2 5.8 - - + -
640A LEU 2.9 14.1 + - - +
641A PHE* 3.3 8.3 + - + +
643A ARG* 1.3 75.7 - - - +
645A HIS* 1.3 60.4 + - - +
648A GLY* 3.1 22.3 + - - -
649A ASP* 3.2 29.1 + - - +
651A VAL* 3.9 15.7 - - + -
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Residues in contact with HIS 645 (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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283A ARG* 3.3 23.1 + - - +
284A PRO* 2.8 31.4 + - - +
285A ALA* 4.3 4.5 - - - +
286A LEU* 3.3 33.9 + - + +
641A PHE 2.9 17.1 + - - +
642A PHE 3.6 3.6 - - - +
644A ALA* 1.3 78.4 - - - +
646A SER* 1.3 58.2 + - - +
777A ASP* 4.7 16.5 + - - -
779A VAL* 3.8 38.7 + - + +
780A ALA* 5.3 2.0 + - - +
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Residues in contact with SER 646 (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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283A ARG* 3.3 18.2 + - - -
642A PHE* 2.8 50.7 + - - -
643A ARG* 3.7 8.5 + - - -
645A HIS* 1.3 78.8 - - - +
647A ARG* 1.3 64.7 + - - +
779A VAL* 4.1 14.6 - - - -
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Residues in contact with ARG 647 (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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275A GLN* 3.3 35.7 - - - +
283A ARG* 3.7 10.2 + - - +
643A ARG* 2.8 57.1 + - - +
646A SER* 1.3 85.0 + - - +
648A GLY* 1.3 56.5 + - - +
649A ASP* 2.8 37.0 + - - +
767A GLU* 4.9 1.8 + - - -
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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