Contacts of the strand formed by residues 555 - 563 (chain B) in PDB entry 1NA8
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 ILE 555 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B PHE* 3.8 30.5 - - + -
549B SER* 3.3 36.3 - - - +
551B ALA* 4.7 0.7 - - + -
553B GLN 4.3 1.8 - - - +
554B PRO* 1.3 78.5 - - - +
556B ARG* 1.3 62.7 + - - +
558B ILE* 3.5 27.7 - - + +
579B GLU* 3.2 4.5 - - - +
580B LEU* 2.8 35.8 + - + +
614B PHE* 3.8 24.2 - - + -
615B THR 3.5 3.8 - - - +
616B MET* 4.1 24.2 - - + -
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Residues in contact with ARG 556 (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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554B PRO* 4.0 30.5 - - + +
555B ILE* 1.3 79.9 - - - +
557B ASN* 1.3 76.7 + - - +
558B ILE* 3.2 3.6 + - - -
578B MET 3.6 0.4 - - - -
579B GLU* 2.7 46.2 + - + +
580B LEU 5.8 0.2 + - - -
614B PHE* 3.6 2.6 - - - +
615B THR* 2.9 40.4 + - - +
617B GLY 6.3 0.4 - - - +
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Residues in contact with ASN 557 (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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556B ARG* 1.3 81.1 - - - +
558B ILE* 1.3 62.7 + - - +
559B VAL* 3.4 11.6 + - - +
578B MET* 3.1 24.8 + - - +
579B GLU* 4.3 1.8 + - - +
613B THR* 3.3 12.1 + - - +
614B PHE* 3.5 3.7 - - - -
615B THR* 3.1 31.0 + - + +
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Residues in contact with ILE 558 (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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523B PHE* 4.1 15.5 - - + -
547B MET* 3.6 30.3 - - + -
555B ILE* 3.5 48.0 - - + +
556B ARG 3.9 1.3 - - - +
557B ASN* 1.3 75.2 - - - +
559B VAL* 1.3 65.3 + - - +
560B PHE 4.4 0.2 + - - -
575B PRO* 5.5 5.0 - - - +
577B GLY 4.9 2.1 - - - +
578B MET* 3.1 32.4 + - - +
579B GLU* 4.0 2.0 - - - -
580B LEU* 4.1 8.7 - - + +
592B ILE* 3.9 19.7 - - + -
612B LEU* 4.4 10.5 - - + -
613B THR 3.3 4.5 - - - -
614B PHE* 3.9 4.7 - - + -
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Residues in contact with VAL 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASN 3.7 11.9 - - - +
558B ILE* 1.3 79.8 - - - +
560B PHE* 1.3 61.1 + - - +
561B GLN* 3.9 31.9 - - + +
578B MET* 6.3 2.0 - - - -
611B LYS 3.5 2.6 - - - +
612B LEU* 3.4 6.9 - - - +
613B THR* 2.9 46.6 + - - +
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Residues in contact with PHE 560 (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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517B VAL* 4.6 2.9 - - + -
525B ILE* 4.0 32.8 - - + -
527B PHE* 3.8 32.3 - + - -
545B VAL* 4.3 13.0 - - + -
547B MET* 3.8 17.0 - - + +
558B ILE* 4.2 1.6 - - - +
559B VAL* 1.3 74.9 - - - +
561B GLN* 1.3 60.0 + - - +
562B SER* 3.4 18.8 - - - -
572B LEU* 3.7 18.2 - - + +
594B GLN* 3.7 25.4 + - - +
596B LEU* 4.5 3.1 - - + -
610B TYR* 3.7 38.8 - + + -
611B LYS 3.8 0.7 - - - -
612B LEU* 4.2 11.9 - - + -
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Residues in contact with GLN 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 VAL* 3.9 24.1 - - + +
560B PHE* 1.3 76.5 - - - +
562B SER* 1.3 70.0 + - - +
572B LEU* 4.0 5.2 - - + -
610B TYR* 3.1 6.9 - - - +
611B LYS* 2.8 51.9 + - + +
613B THR* 5.6 4.4 + - - +
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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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560B PHE* 3.4 19.9 - - - -
561B GLN* 1.3 85.2 + - - +
563B ALA* 1.3 62.0 + - - +
570B VAL* 3.8 18.3 - - - +
572B LEU* 3.8 18.5 - - - +
596B LEU* 4.0 2.0 - - - +
608B LEU* 3.8 28.3 - - - +
609B ARG 3.2 9.4 - - - -
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Residues in contact with ALA 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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562B SER* 1.3 75.6 - - - +
564B VAL* 1.3 65.1 + - - +
570B VAL* 4.0 6.7 - - - -
608B LEU* 3.7 5.5 - - - +
609B ARG* 2.9 40.2 + - + +
611B LYS* 6.3 3.8 - - - -
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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