Contacts of the helix formed by residues 680 - 702 (chain B) in PDB entry 4BEJ
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 MET 680 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ARG* 4.2 13.7 + - - +
679B ASP* 1.3 81.9 + - - +
681B ALA* 1.3 56.9 + - - +
682B GLN* 3.1 18.5 + - + +
683B ARG* 3.3 61.7 + - + +
684B ARG* 4.2 6.6 + - - +
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Residues in contact with ALA 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ARG* 3.9 25.4 - - - +
679B ASP* 3.1 10.6 + - + +
680B MET* 1.3 77.0 - - - +
682B GLN* 1.3 57.3 + - - +
683B ARG 3.3 0.4 - - - -
684B ARG* 3.4 16.5 + - + +
685B LYS* 3.1 23.0 + - - +
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Residues in contact with GLN 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ASP 3.8 17.0 + - - +
680B MET* 4.2 11.4 - - + +
681B ALA* 1.3 76.2 - - - +
683B ARG* 1.3 63.3 + - + +
684B ARG 3.1 1.6 - - - -
685B LYS* 2.9 10.9 + - + +
686B GLU* 2.7 49.5 + - + +
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Residues in contact with ARG 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B LEU* 5.7 0.7 - - + +
322B TYR* 3.7 37.4 + - + +
680B MET* 3.3 51.2 + - + +
681B ALA 3.3 0.8 - - - -
682B GLN* 1.3 88.8 - - + +
684B ARG* 1.3 61.8 + - + +
686B GLU* 3.4 17.9 + - - +
687B ALA* 3.2 20.8 + - - +
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Residues in contact with ARG 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LEU* 5.0 8.4 + - - +
322B TYR* 3.5 30.9 - - + +
323B GLY* 3.4 26.7 - - - +
324B GLU* 3.0 36.9 + - - +
325B PRO* 4.1 5.7 + - - +
326B VAL* 5.4 2.6 - - - +
456B ARG* 4.5 23.3 - - - +
680B MET 4.5 6.5 - - - +
681B ALA* 3.4 14.7 + - - +
683B ARG* 1.3 77.7 - - + +
685B LYS* 1.3 53.4 + - - +
686B GLU 3.3 0.2 - - - -
687B ALA* 3.6 6.4 - - - +
688B ALA* 2.7 35.6 + - - +
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Residues in contact with LYS 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B ALA 3.1 13.0 + - - +
682B GLN* 2.9 15.4 + - + +
684B ARG* 1.3 75.3 - - - +
686B GLU* 1.3 65.2 + - - +
687B ALA 3.1 0.4 - - - -
688B ALA* 4.0 7.6 - - + +
689B ASP* 3.0 53.5 + - - +
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Residues in contact with GLU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.7 0.9 - - - +
682B GLN* 2.7 29.6 + - + +
683B ARG* 3.5 18.9 + - - +
685B LYS* 1.3 79.5 - - - +
687B ALA* 1.3 55.1 + - - +
689B ASP* 4.1 5.3 - - - +
690B MET* 3.1 33.3 + - + +
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Residues in contact with ALA 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR* 5.1 6.6 - - + +
318B LEU* 4.4 23.3 - - + -
319B LEU* 4.9 14.6 - - + +
322B TYR* 4.8 6.5 - - + -
683B ARG 3.2 13.8 + - - +
684B ARG* 3.7 7.9 - - - +
685B LYS 3.1 0.6 - - - -
686B GLU* 1.3 78.3 - - - +
688B ALA* 1.3 60.0 + - - +
689B ASP 3.2 1.6 - - - -
690B MET* 3.9 4.4 - - - +
691B LEU* 2.8 34.7 + - - +
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Residues in contact with ALA 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.2 18.6 - - + +
684B ARG 2.7 18.6 + - - +
685B LYS* 4.0 11.0 - - + +
687B ALA* 1.3 77.4 - - - +
689B ASP* 1.3 62.8 + - - +
691B LEU* 4.0 2.3 - - - +
692B LYS* 3.2 24.9 + - - +
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Residues in contact with ASP 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 6.5 0.7 - - + -
18B VAL* 4.2 17.0 - - + +
685B LYS* 3.0 42.1 + - - +
686B GLU* 4.1 6.7 - - - +
688B ALA* 1.3 75.5 - - - +
690B MET* 1.3 60.5 + - - +
692B LYS* 3.5 5.2 + - - +
693B ALA* 3.0 28.8 + - - +
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Residues in contact with MET 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 5.4 1.9 - - - -
18B VAL* 3.2 42.4 - - + +
19B GLY* 4.4 6.1 - - - +
21B ASP* 5.7 0.4 - - - +
22B ILE* 3.6 40.2 - - + -
315B TYR* 3.3 25.8 - - + +
686B GLU* 3.1 24.5 + - + +
687B ALA* 3.4 4.7 + - - +
689B ASP* 1.3 73.1 - - - +
691B LEU* 1.3 66.8 + - - +
693B ALA* 3.2 5.2 + - - +
694B LEU* 3.0 27.6 + - - +
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Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 4.4 5.8 - - + +
315B TYR* 4.2 13.0 - - + +
316B GLN* 3.5 54.7 - - + +
319B LEU* 4.0 20.6 - - + -
687B ALA 2.8 22.7 + - - +
688B ALA 4.0 3.8 - - - +
690B MET* 1.3 73.2 - - - +
692B LYS* 1.3 66.2 + - + +
694B LEU* 3.3 6.0 + - + +
695B GLN* 3.1 45.1 + - + +
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Residues in contact with LYS 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688B ALA 3.2 17.2 + - - +
689B ASP* 3.7 5.6 - - - +
691B LEU* 1.3 80.9 - - + +
693B ALA* 1.3 64.6 + - - +
695B GLN* 3.0 47.8 - - - +
696B GLY* 3.2 13.4 + - - -
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Residues in contact with ALA 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.7 18.6 - - - +
15B PHE* 3.8 24.0 - - + -
17B THR* 6.2 0.4 - - + -
18B VAL* 3.9 18.2 - - + -
689B ASP 3.0 17.6 + - - +
690B MET* 3.2 5.6 + - - +
692B LYS* 1.3 76.8 - - - +
694B LEU* 1.3 58.6 + - - +
696B GLY* 3.6 1.3 + - - -
697B ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 4.4 14.8 - - + -
22B ILE* 5.3 5.8 - - + -
23B ILE* 5.9 1.1 - - + -
308B ILE* 3.7 39.6 - - + +
311B LEU* 3.8 28.5 - - + +
312B ALA* 3.9 16.3 - - + +
315B TYR* 3.4 39.7 - - + -
690B MET* 3.0 12.4 + - - +
691B LEU* 3.5 6.3 - - - +
693B ALA* 1.3 73.2 - - - +
695B GLN* 1.3 56.9 + - - +
697B ALA* 3.1 5.7 + - - +
698B SER* 2.7 36.3 + - - -
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Residues in contact with GLN 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ALA* 5.5 2.8 - - - +
691B LEU* 3.1 30.8 + - + +
692B LYS* 3.0 50.0 - - - +
694B LEU* 1.3 77.7 - - - +
696B GLY* 1.3 66.0 - - - +
698B SER* 2.6 24.3 + - - -
699B GLN* 3.0 11.1 + - - +
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Residues in contact with GLY 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 5.0 5.6 - - - -
692B LYS* 3.2 15.6 + - - -
693B ALA* 3.9 2.9 - - - -
695B GLN* 1.3 84.9 - - - +
697B ALA* 1.3 62.4 + - - +
699B GLN* 3.1 28.9 - - - +
700B ILE* 3.2 18.0 + - - +
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Residues in contact with ALA 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 19.7 - - + +
14B VAL* 4.2 4.6 - - + +
15B PHE* 3.9 22.9 - - + -
308B ILE* 5.1 8.7 - - + -
693B ALA 2.9 19.5 + - - +
694B LEU* 3.3 6.7 - - - +
696B GLY* 1.3 76.9 - - - +
698B SER* 1.3 61.3 + - - +
700B ILE* 3.0 20.4 + - - +
701B ILE* 3.3 17.1 + - - +
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Residues in contact with SER 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ILE* 3.6 29.6 - - - +
309B ASN* 4.5 7.2 - - - -
694B LEU 2.7 15.2 + - - -
695B GLN* 2.6 27.8 + - - -
697B ALA* 1.3 73.5 - - - +
699B GLN* 1.3 61.2 + - - +
701B ILE* 3.1 21.1 + - - +
702B ALA* 3.6 6.6 + - - +
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Residues in contact with GLN 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B GLN 3.0 11.6 + - - +
696B GLY* 3.1 22.2 - - - +
697B ALA 3.1 0.2 - - - -
698B SER* 1.3 79.4 + - - +
700B ILE* 1.3 58.9 + - + +
702B ALA* 3.5 21.3 + - - +
703B GLU* 5.2 2.9 - - - +
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Residues in contact with ILE 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.1 33.6 - - + +
10B LYS* 3.5 54.7 - - + +
11B LEU* 4.5 8.1 - - + -
14B VAL* 4.2 12.6 - - + -
696B GLY 3.4 15.5 - - - +
697B ALA* 3.0 14.3 + - - +
699B GLN* 1.3 75.8 - - + +
701B ILE* 1.3 61.6 + - - +
702B ALA 3.0 15.8 - - - +
703B GLU 4.5 3.8 - - - +
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Residues in contact with ILE 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 5.0 7.6 - - + -
11B LEU* 4.3 16.2 - - + -
301B LEU* 5.5 13.0 - - + +
304B LEU* 4.0 26.9 - - + -
305B LYS* 3.9 27.8 - - + -
308B ILE* 4.7 11.9 - - + -
309B ASN* 5.8 2.2 - - - +
697B ALA 3.3 12.1 + - - +
698B SER* 3.1 23.3 - - - +
700B ILE* 1.3 72.8 - - - +
702B ALA* 1.3 69.5 + - + +
703B GLU 3.5 7.5 + - - +
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Residues in contact with ALA 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B SER 4.2 6.5 - - - +
699B GLN* 3.5 17.0 + - - +
700B ILE* 3.0 14.3 - - - +
701B ILE* 1.3 87.1 - - + +
703B GLU* 1.3 74.2 + - + +
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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
------------------------------------------------------------
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