Contacts of the helix formed by residues 611 - 620 (chain A) in PDB entry 2NUP
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 ASP 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLU* 4.9 7.9 - - - +
41A LEU* 4.7 2.2 - - - -
43A THR* 4.2 9.2 - - + +
46A LYS* 5.2 11.0 + - - +
454A THR* 4.4 8.1 + - - +
456A THR* 3.5 18.3 + - - +
610A GLN* 1.3 79.3 + - - +
612A LEU* 1.3 70.5 + - - +
613A THR* 4.0 12.0 + - - +
614A GLN* 3.1 28.6 + - - +
615A SER* 3.1 18.2 + - - -
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Residues in contact with LEU 612 (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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12A GLU* 4.1 13.9 + - - +
18A ARG* 3.1 44.4 - - + +
41A LEU* 3.8 23.8 - - + +
520A GLU* 3.7 15.7 - - + +
521A ALA* 3.2 42.4 - - + +
524A ILE* 5.2 1.6 - - + -
611A ASP* 1.3 78.2 - - - +
613A THR* 1.3 85.2 + - + +
615A SER* 2.8 11.9 + - - -
616A LEU* 3.1 20.8 + - + +
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Residues in contact with THR 613 (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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12A GLU* 5.1 8.0 + - - +
18A ARG* 5.1 5.6 - - - +
611A ASP* 3.5 13.1 + - - +
612A LEU* 1.3 93.4 - - + +
614A GLN* 1.3 91.1 + - - +
616A LEU* 2.8 16.6 + - - +
617A ILE* 3.2 16.7 + - - +
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Residues in contact with GLN 614 (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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610A GLN* 3.2 31.4 - - + +
611A ASP* 3.1 20.5 + - - +
613A THR* 1.3 99.1 + - - +
615A SER* 1.3 63.3 + - - +
617A ILE* 3.1 18.4 + - - +
618A MET* 3.0 25.6 + - - +
653A PHE* 3.3 28.6 - - + +
699A ARG* 3.5 14.1 + - - +
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Residues in contact with SER 615 (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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524A ILE* 3.1 31.4 - - - +
528A ARG* 3.8 14.6 + - - -
607A PHE* 3.4 31.5 + - - -
610A GLN* 3.9 6.4 - - - +
611A ASP 3.1 15.0 + - - -
612A LEU 2.8 14.0 + - - -
614A GLN* 1.3 71.4 - - - +
616A LEU* 1.3 60.4 + - - -
618A MET* 3.2 7.0 + - - +
619A ILE* 3.1 19.6 + - - +
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Residues in contact with LEU 616 (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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520A GLU* 3.4 51.6 - - + +
524A ILE* 3.5 23.8 - - + -
580A PHE* 4.3 30.1 - - + -
612A LEU* 3.1 23.7 + - + +
613A THR* 2.8 15.0 + - - +
615A SER* 1.3 72.4 - - - +
617A ILE* 1.3 54.3 + - + +
619A ILE* 3.1 4.3 + - + +
620A GLN* 2.7 39.1 + - - +
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Residues in contact with ILE 617 (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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613A THR* 3.2 10.9 + - - +
614A GLN* 3.1 34.6 + - - +
616A LEU* 1.3 79.2 - - + +
618A MET* 1.3 62.6 + - - +
620A GLN 4.0 6.5 - - - -
621A PRO* 3.1 22.8 - - + +
622A ILE* 3.3 31.0 - - + -
651A ASP* 3.2 39.4 - - + +
653A PHE* 3.6 12.8 + - + +
695A ILE* 5.4 2.0 - - + -
699A ARG* 4.3 8.1 - - - +
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Residues in contact with MET 618 (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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587A SER* 5.8 0.7 - - - -
589A PHE* 3.9 18.2 - - + -
606A HIS 3.9 11.0 - - - +
607A PHE* 3.8 27.6 - - + -
610A GLN* 3.4 34.5 - - + -
614A GLN 3.0 12.0 + - - +
615A SER 3.4 7.0 - - - +
616A LEU 3.1 0.2 - - - -
617A ILE* 1.3 80.7 - - - +
619A ILE* 1.3 63.1 + - - +
621A PRO* 3.5 11.1 - - - +
652A THR* 5.5 2.4 - - - +
653A PHE* 3.2 49.6 - - + +
654A PHE* 3.5 26.8 - - + -
721A LYS* 5.0 7.1 + - - -
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Residues in contact with ILE 619 (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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523A ALA* 4.9 2.5 - - + +
524A ILE* 3.7 19.1 - - + -
527A ALA* 4.0 14.6 - - + -
580A PHE* 3.9 18.4 - - + +
583A HIS* 3.4 20.4 + - + +
584A LEU* 3.8 33.2 - - + +
587A SER* 4.9 4.8 - - - -
589A PHE* 4.2 18.2 - - + -
607A PHE* 3.5 31.9 - - + -
615A SER 3.1 10.7 + - - +
616A LEU* 3.8 4.5 - - + +
618A MET* 1.3 80.3 - - - +
620A GLN* 1.3 61.1 + - + +
621A PRO* 3.7 4.0 - - - +
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Residues in contact with GLN 620 (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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579A GLN* 3.3 32.1 + - - +
580A PHE* 3.2 31.4 - - + -
583A HIS* 2.8 40.6 + - + +
616A LEU* 2.7 19.0 + - + +
617A ILE* 3.4 6.7 - - - +
619A ILE* 1.3 80.9 - - + +
621A PRO* 1.3 70.7 - - - +
622A ILE* 3.5 4.9 + - - +
637A LEU* 4.0 10.5 - - + -
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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