Contacts of the strand formed by residues 511 - 518 (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 SER 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B PRO* 1.3 74.2 - - - +
512B LYS* 1.3 61.4 + - - +
529B ILE* 3.3 7.7 - - - +
530B LEU* 2.7 59.8 + - - +
531B PRO 4.8 3.3 + - - -
532B PRO* 5.4 0.8 - - - +
534B PHE* 5.3 2.6 - - - +
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Residues in contact with LYS 512 (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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475B PRO* 5.8 7.6 - - + -
511B SER* 1.3 79.8 - - - +
513B LYS* 1.3 64.1 + - - +
514B LEU* 3.8 6.0 + - + +
527B GLN* 3.2 40.3 + - + +
528B MET 3.4 7.6 - - - +
529B ILE* 4.6 11.7 - - + -
556B ASP* 3.1 33.9 + - - +
557B THR* 4.1 2.7 - - - -
558B VAL 2.7 30.3 + - - +
559B PHE* 5.9 1.1 - - - -
560B ARG* 4.2 3.6 - - - +
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER 4.2 0.4 - - - -
512B LYS* 1.3 74.1 - - - +
514B LEU* 1.3 61.7 + - - +
515B ASP* 3.9 11.2 + - + -
526B TYR* 3.5 30.5 - - + +
527B GLN* 3.7 4.2 - - - -
528B MET* 2.9 60.0 + - + +
530B LEU* 4.0 23.6 - - + +
534B PHE* 4.5 10.7 - - - -
536B LYS* 5.0 9.1 - - - +
616B MET* 4.6 8.7 - - + +
618B PHE* 4.7 4.8 - - - -
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Residues in contact with LEU 514 (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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425B MET* 3.9 16.6 - - + +
427B GLY* 5.3 3.8 - - - -
512B LYS* 3.8 9.2 + - + +
513B LYS* 1.3 74.1 - - - +
515B ASP* 1.3 62.6 + - - +
525B TRP* 3.6 27.4 - - + -
526B TYR 3.5 15.5 - - - +
527B GLN* 5.3 1.6 - - + +
555B ALA* 4.6 11.4 - - + +
556B ASP* 3.1 33.0 - - - +
557B THR* 3.3 27.6 - - + -
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Residues in contact with ASP 515 (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* 3.9 11.7 - - + -
514B LEU* 1.3 76.1 - - - +
516B PHE* 1.3 92.1 + - - +
525B TRP* 3.4 16.6 - - - -
526B TYR* 3.0 51.7 + - + +
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Residues in contact with PHE 516 (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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515B ASP* 1.3 105.9 - - - +
517B ILE* 1.3 67.2 + - - +
518B ILE* 5.2 6.3 - - + -
523B LYS* 3.2 42.2 - - + -
524B PHE 3.6 15.0 - - - +
525B TRP* 3.7 41.5 - + + -
526B TYR* 3.5 13.6 - - - -
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Residues in contact with ILE 517 (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* 1.3 82.4 - - - +
518B ILE* 1.3 68.2 + - + +
519B LEU* 3.5 20.9 + - + -
523B LYS* 3.1 3.5 - - - -
524B PHE* 2.8 40.1 + - + +
526B TYR* 4.5 10.5 - - + -
578B PHE* 3.5 24.9 - - + -
612B GLN* 2.9 50.7 - - + +
613B PHE* 6.2 1.1 - - + -
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Residues in contact with ILE 518 (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* 5.3 5.6 - - + -
517B ILE* 1.3 80.6 - - + +
519B LEU* 1.3 68.3 + - - +
520B ASN 4.2 0.9 - - - +
521B GLU* 3.3 42.6 - - - +
522B THR 3.4 25.8 - - - +
523B LYS* 4.5 6.3 - - + +
612B GLN* 5.4 0.2 - - - +
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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