Contacts of the strand formed by residues 561 - 568 (chain B) in PDB entry 6NID
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 GLY 561 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493B PHE 3.5 0.2 - - - +
494B GLN* 3.6 18.2 - - - -
495B LYS* 2.6 40.1 + - - +
496B ASN* 4.4 3.9 + - - +
560B ARG* 1.3 74.7 - - - +
562B SER* 1.3 65.4 + - - -
563B ILE* 3.4 3.5 + - - +
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Residues in contact with SER 562 (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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492B GLN* 5.2 4.4 + - - -
493B PHE 3.9 1.1 - - - -
494B GLN* 3.9 7.0 - - - +
540B ASN* 3.5 13.2 + - - +
560B ARG 3.9 1.8 + - - +
561B GLY* 1.3 69.2 - - - -
563B ILE* 1.3 66.5 + - - +
564B THR* 4.2 4.2 + - - -
601B EDO 3.5 23.1 - - - -
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Residues in contact with ILE 563 (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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491B VAL 3.6 1.6 - - - +
492B GLN* 3.4 4.8 - - - +
493B PHE* 2.8 47.6 + - + +
495B LYS* 3.8 20.9 - - + -
501B MET* 5.4 0.4 - - - -
539B ILE* 4.0 19.1 - - + -
540B ASN* 3.3 11.0 - - - +
556B LEU* 4.5 4.5 - - + -
559B MET* 3.7 28.5 - - + -
560B ARG 4.1 10.8 - - - +
561B GLY 3.7 9.0 - - - +
562B SER* 1.3 82.0 - - - +
564B THR* 1.3 63.3 + - - +
565B PHE* 3.6 33.5 + - + -
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Residues in contact with THR 564 (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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490B LEU* 4.1 28.5 - - + -
491B VAL 3.5 2.5 - - - +
492B GLN* 2.7 37.7 + - - +
538B GLU 3.7 0.7 - - - +
539B ILE* 3.5 5.2 - - - +
540B ASN* 2.8 44.7 + - - -
541B GLY 4.7 1.3 + - - +
562B SER* 5.0 4.7 + - - -
563B ILE* 1.3 73.3 - - - +
565B PHE* 1.3 63.8 + - - +
566B LYS* 3.9 1.2 + - + +
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Residues in contact with PHE 565 (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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489B ARG 3.6 0.2 - - - +
490B LEU* 3.4 2.9 - - - -
491B VAL* 2.8 54.8 + - + +
493B PHE* 4.1 19.5 - + + -
501B MET* 3.7 31.4 - - + -
503B ILE* 6.1 1.1 - - + -
524B ILE* 5.3 5.4 - - + -
530B LEU* 5.3 9.4 - - + -
536B ILE* 3.8 35.0 - - + -
538B GLU 3.6 1.6 - - - +
539B ILE* 4.0 16.4 - - + -
556B LEU* 3.8 17.7 - - + -
563B ILE* 3.6 24.0 - - + -
564B THR* 1.3 74.8 - - - +
566B LYS* 1.3 62.0 + - - +
567B ILE* 3.5 18.9 + - + +
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Residues in contact with LYS 566 (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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488B VAL* 3.5 27.4 - - + -
489B ARG 3.6 3.6 - - - -
490B LEU* 3.9 20.6 - - + +
536B ILE* 3.5 2.9 - - - -
537B ARG* 2.6 45.7 + - + -
538B GLU* 3.0 59.3 + - + +
564B THR* 3.9 2.5 + - + +
565B PHE* 1.3 70.6 - - - +
567B ILE* 1.3 53.5 + - - +
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Residues in contact with ILE 567 (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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488B VAL* 3.3 7.8 - - - +
489B ARG* 2.9 50.9 + - + +
491B VAL* 3.9 13.2 - - + -
529B THR* 5.6 1.8 - - + +
530B LEU* 3.7 22.2 - - + -
534B ASP* 3.6 31.9 - - + +
535B GLU 3.1 11.4 - - - +
536B ILE* 4.5 9.6 - - + -
537B ARG* 5.1 0.2 - - - -
565B PHE* 3.7 25.4 - - + +
566B LYS* 1.3 78.6 - - - +
568B VAL* 1.3 62.1 + - - +
569B PRO* 3.6 15.6 - - + +
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Residues in contact with VAL 568 (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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487B ARG* 5.1 10.8 - - + -
488B VAL* 3.8 17.9 - - + -
533B GLY 4.6 0.5 - - - +
534B ASP* 3.6 0.5 - - - -
535B GLU* 2.9 38.5 + - + +
537B ARG* 3.6 48.7 - - + +
567B ILE* 1.3 72.1 - - - +
569B PRO* 1.3 73.8 - - + +
570B SER 3.6 0.9 + - - -
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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