Contacts of the strand formed by residues 523 - 530 (chain B) in PDB entry 1N1M
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 LYS 523 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B GLY 4.1 9.7 + - - -
426B PRO* 5.7 0.4 - - - +
516B PHE* 3.2 45.3 - - + -
517B ILE 3.1 14.1 - - - +
518B ILE* 4.0 5.1 - - + +
522B THR* 1.3 75.3 + - - +
524B PHE* 1.3 64.5 + - - +
525B TRP* 4.0 29.4 + - - +
586B GLN* 4.2 10.6 - - - +
590B ILE* 4.7 4.3 - - - +
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Residues in contact with PHE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B PHE* 4.0 1.3 - - - -
517B ILE* 2.8 34.1 + - + +
519B LEU* 3.8 33.4 - - + -
522B THR* 3.4 30.7 - - + -
523B LYS* 1.3 75.0 - - - +
525B TRP* 1.3 64.1 + - - +
578B PHE* 3.5 22.4 - + + -
579B ASP 3.5 18.4 - - - +
580B GLY* 3.6 9.6 - - - -
581B ARG* 3.7 36.1 - - + -
583B SER* 5.0 0.7 - - - -
586B GLN* 4.8 3.4 - - - -
590B ILE* 4.4 20.0 - - + -
605B ASP* 4.4 1.8 - - - -
780B NAG 4.3 17.0 - - - -
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Residues in contact with TRP 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B LYS 6.0 0.2 - - - -
424B GLY 3.6 20.0 - - - -
425B MET* 3.6 28.5 - - + -
426B PRO* 3.5 30.4 - - + +
427B GLY 5.8 2.0 - - - -
514B LEU* 3.6 26.0 - - + -
515B ASP* 3.4 23.3 - - - +
516B PHE* 3.7 32.4 - + + +
523B LYS* 4.0 26.5 + - - +
524B PHE* 1.3 76.6 - - - +
526B TYR* 1.3 60.7 + - - +
555B ALA* 4.0 14.8 - - + +
578B PHE* 3.8 2.1 - - - -
579B ASP* 3.2 33.4 + - + +
586B GLN* 4.3 12.2 + - - -
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Residues in contact with TYR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B LYS* 3.5 21.6 - - + +
514B LEU* 3.5 14.0 - - - +
515B ASP* 3.0 35.7 + - + +
516B PHE* 3.5 38.8 - - - -
517B ILE* 4.2 10.3 - - + -
525B TRP* 1.3 75.4 - - - +
527B GLN* 1.3 70.1 + - - +
528B MET* 3.7 22.9 - - + -
555B ALA* 3.7 4.0 - - - -
577B SER 3.3 13.2 - - - +
578B PHE* 3.8 14.6 - - + -
613B PHE* 3.6 24.5 - + + -
616B MET* 3.2 28.3 - - + +
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Residues in contact with GLN 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B LYS* 3.2 38.8 + - + +
513B LYS 3.7 4.9 - - - +
514B LEU* 5.4 1.8 - - + -
526B TYR* 1.3 78.6 - - - +
528B MET* 1.3 66.0 + - - +
529B ILE* 4.5 15.8 - - + +
554B LYS* 3.1 17.8 + - - +
555B ALA* 3.7 11.0 - - + -
556B ASP* 2.8 32.7 + - - +
560B ARG* 4.7 7.3 - - - +
575B VAL 4.5 1.3 + - - +
576B ALA* 3.0 8.4 - - - +
577B SER* 2.8 41.7 + - - +
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Residues in contact with MET 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B LYS* 3.4 2.8 - - - +
513B LYS* 2.9 54.5 + - + +
526B TYR* 3.7 23.6 - - + -
527B GLN* 1.3 74.1 - - - +
529B ILE* 1.3 62.8 + - - +
530B LEU* 3.3 28.0 + - + +
542B LEU* 5.4 1.8 - - - -
574B ILE* 3.7 13.9 - - + -
575B VAL 3.6 2.0 - - - -
576B ALA* 3.5 22.2 - - + -
613B PHE* 4.4 16.4 - - - -
616B MET* 4.6 1.3 - - - +
618B PHE* 3.2 41.7 - - + -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B PRO* 4.3 13.2 - - + -
511B SER 3.3 9.4 - - - +
512B LYS* 4.6 16.4 - - + -
527B GLN* 4.5 17.9 - - - +
528B MET* 1.3 73.4 - - - +
530B LEU* 1.3 61.9 + - - +
560B ARG* 6.3 2.2 - - + -
562B ASN* 4.9 6.3 - - - +
564B ALA* 3.7 32.5 - - + +
565B THR* 4.9 3.4 - - - +
568B ALA* 3.7 22.6 - - + +
574B ILE* 3.6 5.2 - - - -
575B VAL* 2.9 43.2 + - + +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B PRO* 3.1 6.8 - - - +
511B SER* 2.7 54.8 + - - +
513B LYS* 4.0 30.7 - - + +
528B MET* 3.3 37.2 - - + +
529B ILE* 1.3 71.6 - - - +
531B PRO* 1.3 68.3 - - + +
534B PHE* 3.8 37.0 - - + -
568B ALA* 4.2 0.4 - - - -
574B ILE* 3.8 24.9 - - + -
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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