Contacts of the helix formed by residues 644 - 657 (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 GLY 644 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643E PRO* 1.3 73.2 - - - +
645E THR* 1.3 62.1 + - - +
647E ALA* 3.8 9.1 - - - +
648E LEU* 3.2 31.4 + - - +
244F LYS* 3.7 24.3 - - - -
81I G 3.2 6.6 + - - -
82I A 2.8 14.0 + - - -
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Residues in contact with THR 645 (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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917C PRO* 6.2 0.3 - - - +
641E TYR* 3.8 22.2 - - + -
642E ARG* 3.1 16.5 + - - +
643E PRO 3.4 1.0 + - - -
644E GLY* 1.3 76.0 - - - +
646E VAL* 1.3 64.6 + - - +
648E LEU* 3.5 9.7 + - - +
649E ARG* 3.2 28.9 + - - +
289J T 3.9 13.0 - - - +
290J G 2.6 33.3 + - - +
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Residues in contact with VAL 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641E TYR* 3.8 22.9 - - + -
645E THR* 1.3 74.1 - - - +
647E ALA* 1.3 60.9 + - - +
649E ARG* 3.1 25.1 + - + +
650E GLU* 2.8 45.4 + - + +
82I A 2.9 31.7 + - + +
83I A 3.7 23.6 - - - +
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Residues in contact with ALA 647 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644E GLY* 3.8 13.9 - - - +
646E VAL* 1.3 76.9 - - - +
648E LEU* 1.3 56.6 + - - +
650E GLU* 3.0 5.5 + - - +
651E ILE* 2.8 33.5 + - - +
239F ARG* 3.6 24.9 - - - +
244F LYS* 3.5 29.4 - - + +
81I G 4.8 2.0 - - - +
82I A 3.1 16.2 + - - +
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Residues in contact with LEU 648 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911C ILE* 4.3 20.1 - - + +
915C LEU* 4.0 18.4 - - + +
916C LEU* 4.9 1.8 - - + -
917C PRO* 3.6 34.1 - - + -
644E GLY 3.2 19.7 + - - +
645E THR* 3.7 8.7 - - - +
646E VAL 3.2 0.2 - - - -
647E ALA* 1.3 74.5 - - - +
649E ARG* 1.3 67.6 + - - +
651E ILE* 3.3 21.8 + - + +
652E ARG* 3.1 49.2 + - - +
244F LYS* 4.1 14.6 - - + +
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Residues in contact with ARG 649 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641E TYR* 3.2 46.5 - - - -
645E THR* 3.2 19.6 + - - +
646E VAL* 3.1 30.9 + - + +
648E LEU* 1.3 78.3 - - - +
650E GLU* 1.3 58.8 + - + +
652E ARG* 3.5 10.5 + - - +
653E ARG* 3.0 28.2 + - + +
7I A 3.3 37.7 + - - -
8I T 3.0 30.3 - - - +
83I A 5.4 1.2 + - - -
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Residues in contact with GLU 650 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646E VAL* 2.8 33.1 + - + +
647E ALA 3.0 8.9 + - - +
649E ARG* 1.3 76.5 - - + +
651E ILE* 1.3 65.0 + - - +
653E ARG* 3.3 7.1 + - - +
654E TYR* 2.9 46.3 + - + -
235F ARG* 5.1 7.0 + - - +
239F ARG* 2.8 45.1 + - + +
82I A 5.3 2.1 + - - -
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Residues in contact with ILE 651 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911C ILE* 3.9 24.7 - - + -
915C LEU* 4.8 0.2 - - + -
647E ALA 2.8 18.4 + - - +
648E LEU* 3.3 25.5 + - + +
650E GLU* 1.3 75.9 - - - +
652E ARG* 1.3 57.7 + - - +
655E GLN* 2.9 54.5 + - - +
239F ARG* 3.7 26.0 - - - +
242F GLY* 3.7 17.5 - - - +
243F VAL 3.6 27.6 - - - +
244F LYS* 4.0 10.1 - - + +
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Residues in contact with ARG 652 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909C PRO* 6.1 0.8 - - - +
911C ILE* 3.2 35.6 - - + +
916C LEU* 4.3 16.4 - - - +
917C PRO* 5.4 2.2 - - - +
648E LEU* 3.1 42.2 + - - +
649E ARG* 3.9 8.3 - - - +
650E GLU 3.3 0.2 - - - -
651E ILE* 1.3 76.2 - - - +
653E ARG* 1.3 62.4 + - - +
655E GLN* 4.1 4.9 - - - +
656E LYS* 3.2 25.9 + - - +
289J T 4.9 10.5 + - - -
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Residues in contact with ARG 653 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649E ARG* 3.0 20.0 + - + +
650E GLU* 3.6 7.4 - - - +
651E ILE 3.2 0.2 - - - -
652E ARG* 1.3 76.9 - - - +
654E TYR* 1.3 104.1 + - + +
656E LYS* 3.2 17.3 + - - +
657E SER* 3.3 16.2 + - - +
659E GLU* 4.7 8.7 + - - -
206J C 5.9 1.4 + - - -
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Residues in contact with TYR 654 (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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650E GLU* 2.9 48.0 + - + +
653E ARG* 1.3 113.2 + - + +
655E GLN* 1.3 62.1 + - - +
656E LYS 3.1 5.4 - - - -
657E SER* 3.2 19.1 + - - +
659E GLU* 4.5 7.0 - - - -
661E LEU* 3.8 20.2 - - + -
236F ARG* 3.5 42.7 - - + +
239F ARG* 3.8 14.1 - - + -
240F ARG* 2.8 48.5 + - + +
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Residues in contact with GLN 655 (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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881C ARG* 3.5 6.4 + - - -
907C VAL* 3.2 32.0 + - + +
908C LEU 4.1 4.8 + - - -
909C PRO* 3.3 19.9 - - + +
910C ASN* 2.7 49.7 + - - +
911C ILE* 4.1 3.6 - - - +
651E ILE* 2.9 31.8 + - - +
652E ARG* 4.2 4.7 - - - +
654E TYR* 1.3 75.8 - - - +
656E LYS* 1.3 59.2 + - - +
657E SER 4.3 1.4 - - - +
705E GLU* 5.9 0.2 + - - -
239F ARG 4.0 4.3 - - - +
240F ARG* 3.3 26.2 + - - +
241F GLY 4.3 0.8 - - - -
242F GLY* 3.7 16.2 - - - +
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Residues in contact with LYS 656 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C ARG* 3.4 21.3 + - - +
909C PRO* 5.1 6.3 - - + -
652E ARG 3.2 17.7 + - - +
653E ARG* 3.4 9.2 - - - +
654E TYR 3.1 0.4 - - - -
655E GLN* 1.3 82.0 - - - +
657E SER* 1.3 57.9 + - - +
658E THR* 4.8 0.2 - - - +
9I C 4.2 18.8 + - - -
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Residues in contact with SER 657 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C ARG* 4.9 0.3 - - - -
906C GLY* 4.1 6.9 - - - -
653E ARG* 3.3 14.3 + - - +
654E TYR* 3.2 16.9 + - - +
655E GLN 4.3 2.6 - - - +
656E LYS* 1.3 78.6 - - - +
658E THR* 1.3 68.0 + - - +
659E GLU* 2.8 28.0 + - - -
240F ARG* 3.1 22.2 + - - -
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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