Contacts of the helix formed by residues 663 - 679 (chain E) in PDB entry 2NQB
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 663 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660E LEU 5.5 4.8 + - - -
661E LEU 4.0 1.8 + - - -
662E ILE* 1.3 84.8 + - + +
664E LYS* 1.3 65.5 + - - +
666E PRO* 3.5 26.2 - - + +
667E PHE* 3.3 17.5 + - - +
228F GLY 5.4 4.7 + - - +
230F THR* 5.7 3.8 - - + +
233F ALA* 5.0 1.0 - - - +
236F ARG* 4.8 5.3 - - - +
90I T 3.4 17.1 + - - +
91I T 3.0 41.8 + - - +
206J C 3.5 41.6 + - - -
207J A 3.9 31.4 + - - +
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Residues in contact with LYS 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660E LEU* 3.3 20.8 - - + +
662E ILE 3.5 3.3 + - - +
663E ARG* 1.3 69.9 - - - +
665E LEU* 1.3 67.9 + - - +
667E PHE* 3.2 4.0 + - - +
668E GLN* 3.0 22.6 + - - +
689E VAL* 5.6 0.9 - - - +
690E MET* 3.2 36.8 - - + +
693E GLN* 4.2 14.6 - - - +
91I T 2.9 25.6 + - - +
92I T 5.5 9.0 - - - +
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Residues in contact with LEU 665 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664E LYS* 1.3 72.4 - - - +
666E PRO* 1.3 69.1 - - + +
668E GLN* 3.2 19.5 + - + +
669E ARG* 3.0 44.9 + - + +
90I T 3.5 26.5 - - + +
91I T 2.9 45.6 + - + +
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Residues in contact with PRO 666 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662E ILE* 5.6 0.4 - - + -
663E ARG* 3.5 30.3 - - + +
664E LYS 3.5 1.3 - - - -
665E LEU* 1.3 94.1 - - + +
667E PHE* 1.3 61.9 + - - +
669E ARG* 3.3 17.3 + - - +
670E LEU* 3.1 22.3 + - - +
225F ASN* 4.6 5.0 - - - +
228F GLY* 3.8 32.8 - - - +
229F ILE* 5.3 1.6 - - - -
90I T 3.7 31.0 - - - +
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Residues in contact with PHE 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662E ILE* 4.1 20.1 - - + +
663E ARG 3.3 15.4 + - - +
664E LYS 3.2 5.2 + - - +
666E PRO* 1.3 78.6 - - - +
668E GLN* 1.3 64.4 + - - +
670E LEU* 3.1 9.1 + - + +
671E VAL* 3.0 44.0 + - + +
689E VAL* 3.8 11.9 - - + -
692E LEU 3.7 3.8 - - - -
693E GLN* 3.4 60.6 - - + -
696E SER* 3.6 24.7 - - - -
229F ILE* 4.4 11.2 - - + -
258F LEU* 4.8 6.3 - - + -
262F LEU* 3.9 21.5 - - + -
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Residues in contact with GLN 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664E LYS 3.0 12.9 + - - +
665E LEU* 3.5 23.1 - - + +
667E PHE* 1.3 77.9 - - - +
669E ARG* 1.3 56.5 + - - +
671E VAL* 3.4 2.8 + - - +
672E ARG* 3.0 59.3 + - - +
686E SER* 5.2 8.5 - - - +
689E VAL* 3.6 45.8 - - + +
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Residues in contact with ARG 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665E LEU* 3.0 37.9 + - + +
666E PRO* 3.7 26.1 - - - +
668E GLN* 1.3 74.0 - - - +
670E LEU* 1.3 61.2 + - - +
672E ARG* 3.3 8.7 + - - +
673E GLU* 2.8 31.4 + - - +
222F LEU* 4.3 16.2 - - + +
225F ASN* 3.1 28.8 + - - +
228F GLY* 5.9 1.6 - - - -
90I T 2.4 43.0 + - - -
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Residues in contact with LEU 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666E PRO 3.1 9.6 + - - +
667E PHE* 3.1 11.6 + - + +
669E ARG* 1.3 80.1 - - - +
671E VAL* 1.3 56.6 + - - +
673E GLU* 3.3 6.7 + - - +
674E ILE* 2.9 51.4 + - + +
225F ASN* 3.8 14.1 - - + +
226F ILE* 3.7 48.9 - - + +
229F ILE* 3.9 22.2 - - + -
258F LEU* 4.3 4.0 - - + -
259F LYS* 5.6 2.9 - - + -
262F LEU* 3.6 27.1 - - + -
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Residues in contact with VAL 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667E PHE* 3.0 47.3 + - + +
668E GLN* 3.6 10.3 - - - +
669E ARG 3.3 0.2 - - - -
670E LEU* 1.3 77.6 - - - +
672E ARG* 1.3 57.5 + - + +
674E ILE* 3.9 0.4 - - - -
675E ALA* 2.9 28.1 + - - +
684E PHE* 3.8 23.1 - - + -
689E VAL* 4.8 8.7 - - + -
692E LEU* 3.6 30.7 - - + -
262F LEU* 4.5 11.0 - - + -
266F ILE* 3.9 12.8 - - + +
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Residues in contact with ARG 672 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E GLN* 3.0 54.3 + - + +
669E ARG* 3.8 7.4 - - - +
671E VAL* 1.3 79.1 - - + +
673E GLU* 1.3 57.1 + - - +
675E ALA* 3.9 4.1 - - - +
676E GLN* 2.9 31.9 + - - +
682E LEU 4.7 6.1 + - - -
684E PHE* 3.8 34.7 + - + +
689E VAL* 5.3 0.4 - - + -
222F LEU* 3.8 16.3 - - + +
197J A 3.0 48.4 + - - +
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Residues in contact with GLU 673 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669E ARG 2.8 16.4 + - - +
670E LEU* 3.6 10.5 - - - +
671E VAL 3.3 0.2 - - - -
672E ARG* 1.3 74.7 - - - +
674E ILE* 1.3 67.8 + - - +
676E GLN* 3.3 6.5 + - - +
677E ASP* 3.1 36.4 + - - +
222F LEU* 3.7 28.4 - - + +
223F ARG* 3.2 5.1 - - - -
224F ASP* 3.9 10.4 + - - -
225F ASN* 2.3 56.3 + - - +
226F ILE* 4.9 2.4 + - - +
259F LYS* 4.9 12.6 + - - -
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Residues in contact with ILE 674 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670E LEU* 2.9 42.6 + - + +
671E VAL 4.0 2.2 - - - +
673E GLU* 1.3 81.7 - - + +
675E ALA* 1.3 64.0 + - - +
677E ASP* 3.1 19.6 + - - +
678E PHE* 3.3 10.9 + - + +
259F LYS* 4.2 28.0 - - + -
262F LEU* 3.9 26.9 - - + -
263F GLU* 4.0 28.0 - - + +
266F ILE* 3.7 20.6 - - + -
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Residues in contact with ALA 675 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671E VAL 2.9 19.2 + - - +
672E ARG 3.9 1.8 - - - +
674E ILE* 1.3 77.0 - - - +
676E GLN* 1.3 57.8 + - - +
678E PHE* 2.9 5.6 + - - +
679E LYS 2.8 30.3 + - - +
682E LEU* 4.0 13.8 - - + +
684E PHE* 3.5 31.2 - - + -
266F ILE* 3.8 22.0 - - + +
270F VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 676 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672E ARG 2.9 18.6 + - - +
673E GLU* 3.5 5.0 - - - +
675E ALA* 1.3 76.1 - - - +
677E ASP* 1.3 66.7 + - - +
678E PHE 3.2 0.9 + - - -
679E LYS* 3.3 22.2 + - - +
680E THR* 3.8 21.8 + - + +
681E ASP 5.7 2.9 - - - +
682E LEU* 6.0 0.6 - - - +
219F ARG* 5.1 17.2 - - - +
222F LEU* 3.7 36.2 + - - +
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Residues in contact with ASP 677 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673E GLU* 3.1 28.9 + - - +
674E ILE* 3.1 12.8 + - - +
676E GLN* 1.3 81.7 - - - +
678E PHE* 1.3 59.1 + - - +
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Residues in contact with PHE 678 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674E ILE* 3.3 7.2 + - + +
675E ALA* 2.9 11.0 + - - +
677E ASP* 1.3 79.9 - - - +
679E LYS* 1.3 65.8 + - + +
266F ILE* 5.3 4.5 - - + -
267F ARG* 3.5 52.3 - - + -
270F VAL* 3.5 35.9 - - + -
271F THR* 4.0 9.4 - - - -
274F GLU* 4.2 10.1 - - - -
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Residues in contact with LYS 679 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675E ALA 2.8 16.0 + - - +
676E GLN* 3.3 12.8 + - - -
678E PHE* 1.3 83.5 - - + +
680E THR* 1.3 88.0 + - - +
681E ASP* 4.1 2.2 + - - +
682E LEU* 3.5 34.5 + - + +
270F VAL* 3.9 9.9 - - + -
274F GLU* 3.1 38.4 - - - +
279F LYS* 6.3 1.4 - - - +
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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