Contacts of the helix formed by residues 518 - 535 (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 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.4 26.0 - - + +
18A ARG* 3.3 32.1 + - - +
19A PHE 3.1 24.5 + - - +
20A SER 3.2 8.2 + - - +
22A ASN* 4.8 4.3 + - - +
516A SER 3.6 0.4 + - - -
517A PHE* 1.3 73.6 - - - +
519A GLN* 1.3 54.2 + - - +
520A GLU* 3.6 5.2 + - - +
521A ALA* 3.1 31.5 + - - +
522A ALA* 2.8 36.2 + - - +
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Residues in contact with GLN 519 (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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517A PHE* 3.4 23.4 - - + +
518A ASP* 1.3 73.1 + - - +
520A GLU* 1.3 65.8 + - + +
522A ALA* 3.5 1.2 + - - +
523A ALA* 2.9 29.5 + - - +
572A GLU 3.4 10.2 + - - +
573A THR* 2.9 33.5 - - - +
574A PHE 3.3 13.9 - - - -
576A LEU* 3.2 39.7 + - - +
577A TYR* 3.9 18.0 - - + +
580A PHE* 4.4 7.3 - - + -
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Residues in contact with GLU 520 (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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18A ARG* 2.8 27.4 + - - -
518A ASP* 3.2 4.2 - - - +
519A GLN* 1.3 83.7 + - + +
521A ALA* 1.3 68.5 + - - +
523A ALA* 2.9 14.3 + - - +
524A ILE* 3.1 15.2 + - - +
576A LEU* 5.8 1.6 - - - +
580A PHE* 4.0 26.0 - - + -
612A LEU* 3.7 16.1 - - + +
616A LEU* 3.4 30.8 - - + +
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Residues in contact with ALA 521 (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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18A ARG* 4.2 11.9 - - + +
19A PHE 3.5 19.1 - - - +
41A LEU* 4.5 2.8 - - + +
518A ASP* 3.1 33.0 + - - +
520A GLU* 1.3 78.8 - - - +
522A ALA* 1.3 57.5 + - - +
524A ILE* 3.5 2.9 + - - +
525A LEU* 3.0 35.3 + - + +
612A LEU* 3.2 18.5 - - + +
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Residues in contact with ALA 522 (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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20A SER* 4.3 9.1 - - - +
36A VAL* 3.9 16.2 - - + -
517A PHE* 3.5 33.0 - - + -
518A ASP 2.8 20.8 + - - +
519A GLN 3.8 0.9 - - - +
521A ALA* 1.3 71.2 - - - +
523A ALA* 1.3 55.5 + - - +
525A LEU* 3.1 5.7 + - - -
526A MET* 2.6 41.2 + - - +
577A TYR* 4.2 3.6 - - + -
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Residues in contact with ALA 523 (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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519A GLN 2.9 17.9 + - - +
520A GLU* 2.9 6.5 + - - +
522A ALA* 1.3 74.5 - - - +
524A ILE* 1.3 65.5 + - + +
526A MET* 3.5 2.1 + - - +
527A ALA* 3.0 28.6 + - - +
577A TYR* 4.0 14.3 - - + -
580A PHE* 3.9 33.0 - - + -
581A MET* 4.5 7.1 - - + +
584A LEU* 4.5 4.7 - - + +
616A LEU* 5.1 0.4 - - + -
619A ILE* 4.9 1.7 - - + +
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Residues in contact with ILE 524 (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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41A LEU* 3.4 38.4 - - + -
520A GLU 3.1 8.7 + - - +
521A ALA 4.0 4.3 - - - +
523A ALA* 1.3 79.4 - - + +
525A LEU* 1.3 59.1 + - - +
527A ALA* 3.2 4.7 + - - +
528A ARG* 2.8 43.4 + - - +
607A PHE* 4.0 5.9 - - + -
612A LEU* 4.6 3.4 - - + +
615A SER* 3.1 29.8 - - - +
616A LEU* 3.5 33.0 - - + +
619A ILE* 3.7 24.5 - - + -
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Residues in contact with LEU 525 (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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18A ARG 4.4 4.9 - - - +
20A SER* 3.9 17.5 - - - +
36A VAL* 5.6 1.8 - - + -
37A PRO* 6.2 0.7 - - + -
39A ALA* 3.3 47.8 - - + +
40A ALA* 4.0 9.2 - - - +
41A LEU* 3.5 26.0 - - + -
458A ALA* 3.6 20.0 - - + -
460A TYR* 2.7 28.1 + - + +
521A ALA 3.0 27.5 + - - +
522A ALA* 3.6 4.3 - - - +
524A ILE* 1.3 75.2 - - - +
526A MET* 1.3 66.7 + - + +
528A ARG* 3.4 5.3 + - - +
529A LEU* 3.5 8.1 + - - +
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Residues in contact with MET 526 (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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35A VAL 4.5 2.7 - - - +
36A VAL* 3.8 18.8 - - + -
37A PRO* 3.7 30.3 - - + -
522A ALA 2.6 23.7 + - - +
523A ALA* 3.9 4.7 - - - +
525A LEU* 1.3 74.6 - - - +
527A ALA* 1.3 61.2 - - - +
529A LEU* 3.5 7.5 + - - +
530A ALA* 3.2 17.5 + - - +
545A TRP* 3.3 48.6 - - + -
546A LEU* 4.0 11.7 - - + +
549A GLN* 4.2 21.8 - - + -
577A TYR* 3.2 25.6 - - + +
581A MET* 5.0 4.0 - - + -
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Residues in contact with ALA 527 (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 3.0 19.2 + - - +
524A ILE 3.4 4.7 - - - +
525A LEU 3.2 0.2 - - - -
526A MET* 1.3 76.9 - - - +
528A ARG* 1.3 65.4 + - - +
530A ALA* 3.2 3.2 + - - +
531A ILE* 3.0 29.1 + - - +
584A LEU* 3.6 35.4 - - + +
607A PHE* 3.9 20.6 - - + -
619A ILE* 4.0 3.1 - - + -
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Residues in contact with ARG 528 (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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41A LEU* 4.2 8.0 - - - +
420A ILE* 3.4 39.6 + - + +
456A THR* 2.7 37.4 + - - +
457A LEU 4.3 2.0 - - - -
458A ALA* 3.8 8.9 - - + +
460A TYR* 3.1 21.1 - - - +
524A ILE* 2.8 26.4 + - - +
525A LEU* 3.4 3.1 - - - +
527A ALA* 1.3 78.0 - - - +
529A LEU* 1.3 56.8 + - - +
531A ILE* 4.1 0.3 - - - -
532A TYR* 3.0 31.7 + - - +
607A PHE* 2.9 27.2 + - - -
608A MET* 3.3 35.2 + - + +
610A GLN 3.7 16.0 + - - -
615A SER* 3.8 9.9 + - - -
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Residues in contact with LEU 529 (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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37A PRO* 4.1 15.7 - - + -
420A ILE* 3.6 8.5 - - + -
438A ILE* 3.2 38.6 - - + -
460A TYR* 3.4 37.0 - - + +
525A LEU 3.5 5.8 + - - +
526A MET* 3.7 9.6 - - - +
527A ALA 3.2 0.2 - - - -
528A ARG* 1.3 80.0 - - - +
530A ALA* 1.3 59.7 + - - +
532A TYR* 3.5 2.8 + - + +
533A ARG* 3.0 47.3 + - - +
545A TRP* 4.0 26.2 - - + -
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Residues in contact with ALA 530 (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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526A MET 3.2 11.6 + - - +
527A ALA* 3.2 9.4 + - - +
529A LEU* 1.3 79.7 - - - +
531A ILE* 1.3 58.8 + - + +
533A ARG* 3.1 5.8 + - - +
534A ALA* 2.8 27.5 + - - +
542A VAL* 3.6 27.1 - - + +
545A TRP* 4.2 5.1 - - + -
546A LEU* 4.0 25.4 - - + -
590A LEU* 4.3 8.7 - - + -
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Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A ALA 3.0 12.1 + - - +
528A ARG 4.2 1.8 - - - +
530A ALA* 1.3 73.0 - - + +
532A TYR* 1.3 56.7 + - - +
534A ALA* 4.1 5.8 - - - -
535A GLU* 2.7 36.6 + - - +
584A LEU* 4.7 5.8 - - + -
589A PHE* 3.5 29.2 - - + -
590A LEU* 3.9 17.3 - - + -
604A ARG* 3.7 38.4 - - + +
607A PHE* 3.5 36.1 - - + -
608A MET* 4.3 13.9 - - + -
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Residues in contact with TYR 532 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ILE* 3.7 27.8 - - + -
438A ILE* 5.6 1.3 - - + -
439A GLY* 3.3 46.9 + - - -
440A THR* 5.0 2.5 - - - -
528A ARG 3.0 21.0 + - - +
529A LEU* 3.7 4.7 - - + +
531A ILE* 1.3 77.7 - - - +
533A ARG* 1.3 70.3 + - + +
535A GLU* 4.0 5.0 - - + -
536A THR* 3.1 45.2 + - + +
608A MET* 4.9 4.4 - - - -
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Residues in contact with ARG 533 (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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438A ILE* 6.3 1.0 - - - +
529A LEU* 3.0 38.5 + - + +
530A ALA* 3.5 7.0 - - - +
532A TYR* 1.3 83.3 - - + +
534A ALA* 1.3 61.8 + - - +
536A THR* 2.9 6.1 - - - -
537A GLU* 2.7 30.7 + - - -
542A VAL* 4.3 15.8 - - + +
545A TRP* 3.3 62.0 - - - +
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Residues in contact with ALA 534 (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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530A ALA 2.8 16.6 + - - +
531A ILE* 3.5 4.9 - - - +
533A ARG* 1.3 73.3 - - - +
535A GLU* 1.3 58.8 + - - +
536A THR 2.9 9.2 + - - -
537A GLU* 3.1 20.1 + - - +
542A VAL* 4.2 13.6 - - + +
590A LEU* 3.9 21.3 - - + +
604A ARG* 3.9 15.6 + - - +
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Residues in contact with GLU 535 (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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361A LYS* 4.0 37.6 + - - +
365A ASN* 4.5 11.4 + - - -
531A ILE* 2.7 24.2 + - - +
532A TYR* 4.3 5.5 - - + +
534A ALA* 1.3 72.1 - - - +
536A THR* 1.3 62.4 + - - +
537A GLU* 3.8 2.7 - - - +
601A SER* 4.5 8.5 + - - +
604A ARG* 3.4 47.1 - - - +
605A HIS 5.2 0.3 + - - -
608A MET* 5.0 8.1 - - - +
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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