Contacts of the helix formed by residues 485 - 502 (chain A) in PDB entry 1F7V
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 THR 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A ALA* 5.7 0.7 - - - -
460A ILE* 4.4 3.8 - - - -
464A GLN* 4.9 2.7 - - - +
480A SER* 3.7 25.6 - - - +
481A PHE 3.1 19.2 + - - -
482A GLU 3.3 27.4 - - - +
483A GLY 2.8 5.9 + - - +
484A ASP* 1.3 77.5 - - - +
486A GLY* 1.3 67.4 + - - +
487A PRO* 3.1 15.0 - - - +
488A TYR* 2.7 20.1 + - - +
489A LEU 3.4 1.9 + - - -
555A PHE* 3.7 10.4 - - - -
924B G 5.7 0.7 - - - +
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Residues in contact with GLY 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A SER* 3.4 31.5 + - - -
457A ALA* 4.2 2.6 + - - +
460A ILE* 3.6 22.5 - - - +
485A THR* 1.3 69.8 - - - +
487A PRO* 1.3 73.3 - - - +
489A LEU* 2.9 20.0 + - - +
490A GLN* 3.0 11.3 + - - +
601A LEU* 5.4 0.2 - - - -
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Residues in contact with PRO 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A MET* 4.2 3.6 - - - -
453A VAL* 4.1 18.6 - - + -
456A SER* 3.6 2.9 - - - +
457A ALA* 3.7 23.6 - - + -
480A SER 3.9 2.9 - - - +
481A PHE* 3.6 33.0 - - + +
485A THR* 3.1 15.9 - - - +
486A GLY* 1.3 87.4 - - - +
488A TYR* 1.3 52.6 + - - +
490A GLN* 3.5 9.4 - - + +
491A TYR* 2.7 38.4 + - - +
607A MET* 4.5 1.8 - - - +
938B A 3.8 13.7 - - + +
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Residues in contact with TYR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PHE 4.2 1.9 + - - +
483A GLY* 3.3 22.2 - - - +
484A ASP* 5.1 0.2 - - - -
485A THR* 2.7 22.1 + - - +
487A PRO* 1.3 74.4 - - - +
489A LEU* 1.3 63.2 + - - +
491A TYR* 3.3 6.2 + + - +
492A ALA* 3.0 24.0 + - + +
555A PHE* 3.5 16.8 - + - -
558A THR* 3.2 30.5 - - - -
559A HIS* 2.9 33.0 + + - -
562A SER* 3.4 15.1 + - - -
938B A 4.6 4.0 - - - -
939B C 3.6 36.8 - - - +
940B C 2.7 30.7 + - - -
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ILE* 4.0 29.6 - - + -
485A THR 4.4 0.2 - - - +
486A GLY 2.9 8.3 + - - +
488A TYR* 1.3 79.2 - - - +
490A GLN* 1.3 58.9 + - - +
492A ALA* 3.2 6.7 + - - +
493A HIS* 2.9 29.6 + - - +
551A VAL* 5.3 0.7 - - + -
554A LEU* 3.7 32.5 - - + +
555A PHE* 3.9 26.9 - - + -
558A THR* 3.5 34.5 - - + +
592A LEU* 3.6 7.3 - - + +
596A MET* 4.2 21.3 - - + -
601A LEU* 4.6 2.5 - - + -
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Residues in contact with GLN 490 (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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452A LEU 3.5 21.6 + - - -
453A VAL* 4.6 7.6 - - + -
456A SER* 3.5 28.4 - - - +
486A GLY 3.0 7.5 + - - +
487A PRO* 3.5 10.8 - - + +
489A LEU* 1.3 77.1 - - - +
491A TYR* 1.3 51.7 + - - +
493A HIS* 3.2 4.1 + - - +
494A SER* 2.7 30.5 + - - -
596A MET* 3.5 13.6 - - + +
602A THR 3.0 23.8 + - - +
603A PRO* 3.5 4.5 - - - +
604A VAL* 3.1 37.8 + - + +
607A MET* 2.8 20.0 - - + +
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Residues in contact with TYR 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PRO 2.7 17.2 + - - +
488A TYR* 3.6 4.0 - + - +
490A GLN* 1.3 69.9 - - - +
492A ALA* 1.3 61.3 + - - +
494A SER* 3.6 0.7 - - - -
495A ARG* 2.8 62.6 + - - +
607A MET* 3.2 18.3 - - + +
936B G 2.8 47.3 + + - -
937B A 3.4 8.1 - - - -
938B A 2.8 80.6 + + + +
939B C 4.1 12.8 - - - -
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Residues in contact with ALA 492 (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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488A TYR* 3.0 16.6 + - + +
489A LEU 3.4 8.7 - - - +
491A TYR* 1.3 74.3 - - - +
493A HIS* 1.3 68.8 + - - +
495A ARG* 3.3 11.4 + - - +
496A LEU* 3.0 30.4 + - + +
558A THR* 3.9 28.5 - - + +
561A VAL* 5.3 8.5 - - + -
562A SER* 5.0 9.0 - - - +
592A LEU* 4.1 4.0 - - + -
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Residues in contact with HIS 493 (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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489A LEU 2.9 12.8 + - - +
490A GLN* 3.5 9.6 - - - +
492A ALA* 1.3 77.0 - - - +
494A SER* 1.3 63.1 + - - +
496A LEU* 3.3 6.0 + - - +
497A ARG* 3.2 32.0 + - + +
589A ARG* 2.5 43.8 + - + +
592A LEU* 3.6 15.4 - - + +
593A TYR* 3.6 19.3 - + - -
596A MET* 4.4 4.3 - - - -
603A PRO* 3.4 33.0 - - + +
604A VAL 3.1 19.0 + - - +
605A GLU* 4.1 11.4 - - - -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLN 2.7 9.0 + - - -
491A TYR* 3.6 4.3 - - - -
492A ALA 3.2 0.2 - - - -
493A HIS* 1.3 75.3 - - - +
495A ARG* 1.3 56.7 + - - +
497A ARG* 3.5 1.4 + - - +
498A SER* 3.2 22.3 + - - -
604A VAL 3.6 14.4 - - - -
605A GLU 3.2 19.8 + - - +
606A ARG* 3.5 5.2 - - - -
607A MET* 3.2 32.2 + - - -
936B G 3.0 27.0 + - - +
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TYR* 2.8 39.7 + - + +
492A ALA* 3.7 10.0 - - - +
494A SER* 1.3 70.5 - - - +
496A LEU* 1.3 67.3 + - + +
497A ARG 3.1 1.6 - - - -
498A SER* 3.4 2.3 + - - -
499A VAL* 3.1 28.1 + - - +
562A SER* 4.2 16.1 + - - +
565A TYR* 3.3 47.3 + - + +
566A ASP* 5.4 0.8 + - - -
936B G 3.0 46.9 + - + +
937B A 3.4 17.8 + - - -
939B C 2.6 47.1 + - - -
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Residues in contact with LEU 496 (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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492A ALA* 3.0 22.9 + - + +
493A HIS* 3.8 5.8 - - - +
495A ARG* 1.3 79.8 - - + +
497A ARG* 1.3 61.7 + - - +
499A VAL* 3.5 7.7 + - + +
500A GLU* 3.2 26.4 + - - +
561A VAL* 3.9 26.0 - - + -
565A TYR* 5.0 8.5 - - + -
585A TYR* 3.3 46.5 - - + +
588A ALA* 4.4 4.9 - - + -
589A ARG* 3.8 41.3 - - + +
592A LEU* 5.0 5.8 - - + -
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Residues in contact with ARG 497 (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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493A HIS* 3.2 20.5 + - + +
494A SER 3.5 9.4 - - - +
496A LEU* 1.3 76.2 - - - +
498A SER* 1.3 65.6 + - - +
500A GLU* 2.9 26.8 + - - +
501A ARG* 2.9 36.8 + - - +
508A GLN* 6.0 2.4 - - - +
589A ARG* 3.3 44.6 - - - +
605A GLU* 3.3 48.4 + - - +
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Residues in contact with SER 498 (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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439A LYS* 4.3 3.8 + - - -
494A SER 3.2 4.0 + - - -
495A ARG 3.6 7.2 - - - -
496A LEU 3.4 0.4 - - - -
497A ARG* 1.3 79.0 - - - +
499A VAL* 1.3 52.7 + - - +
501A ARG* 3.3 30.0 + - - +
502A ASN* 2.7 36.7 + - - +
936B G 2.4 54.3 + - - -
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Residues in contact with VAL 499 (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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495A ARG 3.1 15.5 + - - +
496A LEU* 3.5 13.0 - - + +
497A ARG 3.1 0.4 - - - -
498A SER* 1.3 77.6 - - - +
500A GLU* 1.3 64.3 + - + +
502A ASN* 3.2 14.2 + - - +
503A ALA* 3.2 8.8 + - - +
565A TYR* 3.6 26.7 - - + +
570A VAL* 3.8 31.2 - - + -
582A LEU* 4.6 3.9 - - + +
585A TYR* 5.2 9.0 - - + -
935B C 3.6 37.2 - - + +
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Residues in contact with GLU 500 (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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496A LEU 3.2 11.1 + - - +
497A ARG* 2.9 31.1 + - - +
499A VAL* 1.3 75.3 - - + +
501A ARG* 1.3 58.4 + - + +
503A ALA* 2.8 34.3 + - - +
504A SER* 3.5 2.1 + - - -
508A GLN* 5.1 5.5 + - - -
511A TRP* 3.9 32.6 - - + -
582A LEU* 4.3 13.9 - - + +
585A TYR* 6.3 1.6 - - + -
586A GLY* 4.5 8.9 - - - +
589A ARG* 3.2 36.6 + - - +
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Residues in contact with ARG 501 (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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442A GLN* 5.7 1.4 + - - -
494A SER 4.2 0.8 + - - -
497A ARG* 2.9 23.3 + - - +
498A SER* 3.3 42.0 + - - +
500A GLU* 1.3 73.0 - - + +
502A ASN* 1.3 58.5 + - - +
503A ALA 2.9 4.2 + - - -
504A SER* 2.9 26.8 + - - +
605A GLU* 3.4 29.4 + - - +
606A ARG* 3.4 46.6 - - - +
936B G 5.3 2.2 + - - -
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Residues in contact with ASN 502 (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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498A SER* 2.7 22.4 + - - +
499A VAL* 3.2 8.1 + - - +
500A GLU 3.1 0.4 - - - -
501A ARG* 1.3 73.0 - - - +
503A ALA* 1.3 59.9 + - - +
504A SER 3.8 0.8 + - - -
570A VAL* 5.3 0.2 - - - +
571A ALA* 3.7 13.9 - - - +
935B C 3.1 55.0 + - - +
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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