Contacts of the strand formed by residues 560 - 565 (chain B) in PDB entry 4NPJ
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 PRO 560 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LEU* 4.0 16.2 - - + -
558B PRO* 3.3 17.0 - - + +
559B ASN* 1.3 83.5 - - - +
561B VAL* 1.3 58.9 + - - +
575B ILE* 3.8 0.2 - - - -
576B ARG* 2.9 47.4 + - + +
579B THR* 3.1 22.4 - - + +
582B PRO* 3.8 27.8 - - + -
584B TRP* 3.7 9.6 + - + -
604B VAL* 4.5 2.2 - - + -
605B ARG 3.4 7.2 - - - +
613B LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 561 (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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559B ASN 4.6 0.2 - - - +
560B PRO* 1.3 76.4 - - - +
562B VAL* 1.3 71.6 + - - +
563B GLN* 5.4 0.3 - - - +
572B GLU* 4.6 19.1 - - - +
573B SER* 3.3 28.9 - - - +
574B LYS 3.5 11.2 - - - +
575B ILE* 4.1 14.8 - - + +
584B TRP* 4.3 0.9 - - - -
603B GLU 4.1 0.3 - - - +
604B VAL* 3.7 2.1 - - - +
605B ARG* 3.0 45.7 + - + +
607B GLU* 4.1 26.7 - - + +
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Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 3.6 19.7 - - + -
561B VAL* 1.3 73.7 - - - +
563B GLN* 1.3 64.1 + - - +
564B MET* 3.9 18.4 - - + +
572B GLU* 3.2 9.6 - - - +
573B SER* 3.0 35.4 + - - +
584B TRP* 3.3 41.7 - - + -
602B VAL* 3.8 27.1 - - + -
603B GLU 3.9 4.3 - - - +
604B VAL* 4.6 5.4 - - + +
646B ILE* 4.4 9.2 - - + -
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Residues in contact with GLN 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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561B VAL 5.4 0.4 - - - +
562B VAL* 1.3 73.9 - - - +
564B MET* 1.3 62.6 + - - +
565B SER* 5.3 2.7 + - - +
570B ALA* 5.0 11.9 - - + -
571B GLN 3.6 4.3 - - - +
572B GLU* 3.3 27.7 - - + +
601B GLU 3.8 1.6 - - - +
602B VAL* 3.5 4.2 - - - +
603B GLU* 2.9 64.0 + - + +
605B ARG* 4.8 15.3 - - + +
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Residues in contact with MET 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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540B LEU* 3.8 29.8 - - + -
542B LEU* 4.4 4.9 - - + -
562B VAL* 3.9 33.2 - - + +
563B GLN* 1.3 76.2 - - - +
565B SER* 1.3 61.5 + - - +
570B ALA* 3.1 3.4 - - - -
571B GLN 2.7 55.5 + - - +
573B SER 4.0 3.8 - - - +
588B PHE* 3.5 50.5 - - + -
590B PHE* 3.6 19.0 - - + -
600B LEU* 4.5 1.8 - - + -
601B GLU 3.7 3.6 - - - -
602B VAL* 4.4 10.8 - - + -
648B MET* 5.1 0.7 - - + -
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Residues in contact with SER 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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563B GLN* 5.3 2.6 + - - +
564B MET* 1.3 75.9 - - - +
566B VAL* 1.3 68.2 + - - +
567B GLY 3.9 9.5 + - - -
568B HIS 5.2 0.2 - - - -
569B LYS 3.2 17.7 - - - -
570B ALA* 3.7 12.3 - - - -
590B PHE* 4.2 2.9 - - - -
600B LEU* 3.7 3.0 - - - +
601B GLU* 2.9 48.1 + - - +
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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