Contacts of the strand formed by residues 555 - 563 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A PHE* 3.6 35.4 - - + -
549A SER* 3.5 27.8 - - - +
551A ALA* 4.7 0.9 - - + -
553A GLN 4.3 4.5 - - - +
554A PRO* 1.3 75.5 - - - +
556A ARG* 1.3 63.9 + - - +
558A ILE* 3.4 28.9 - - + -
579A GLU* 3.1 6.1 - - - +
580A LEU* 2.8 42.7 + - + +
614A PHE* 3.8 20.6 - - + -
615A THR 3.4 5.4 - - - +
616A MET* 3.6 24.7 - - + -
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Residues in contact with ARG 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A PRO* 4.9 16.8 - - + -
555A ILE* 1.3 78.3 - - - +
557A ASN* 1.3 86.5 + - - +
558A ILE* 3.3 3.3 + - - -
578A MET 3.7 2.2 - - - -
579A GLU* 4.5 11.9 - - + +
614A PHE* 3.9 0.9 - - - -
615A THR* 2.8 62.4 + - - +
617A GLY* 3.3 28.6 + - - +
618A ASP* 5.3 0.8 + - - +
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Residues in contact with ASN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ARG* 1.3 93.0 - - - +
558A ILE* 1.3 62.1 + - - +
559A VAL* 3.7 3.3 + - - +
578A MET* 3.0 28.0 + - + +
579A GLU* 5.0 0.8 - - - +
613A THR* 3.3 16.5 - - - +
614A PHE* 4.0 2.6 - - - -
615A THR* 4.6 7.9 + - - +
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Residues in contact with ILE 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A PHE* 3.8 21.1 - - + -
547A MET* 3.6 29.5 - - + +
555A ILE* 3.4 42.6 - - + +
556A ARG 4.3 0.9 - - - +
557A ASN* 1.3 72.6 - - - +
559A VAL* 1.3 65.8 + - - +
575A PRO* 5.2 3.6 - - - +
577A GLY 4.8 0.9 - - - +
578A MET* 2.9 42.3 + - - +
579A GLU* 4.2 0.4 - - - -
580A LEU* 4.1 10.8 - - + -
592A ILE* 3.7 21.3 - - + -
612A LEU* 4.5 4.7 - - + -
613A THR 3.3 7.9 - - - +
614A PHE* 4.0 5.8 - - + -
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Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A MET* 5.8 0.2 - - - -
557A ASN 3.7 3.3 + - - +
558A ILE* 1.3 79.2 - - - +
560A PHE* 1.3 64.3 + - - +
561A GLN* 3.7 35.2 - - + +
575A PRO* 6.2 1.8 - - - -
578A MET* 3.4 22.0 - - + -
611A LYS 3.8 0.9 - - - +
612A LEU* 3.5 5.8 - - - +
613A THR* 2.9 43.6 + - - +
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Residues in contact with PHE 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A VAL* 4.4 3.4 - - + -
525A ILE* 4.1 16.6 - - + -
527A PHE* 3.6 36.1 - + - -
545A VAL* 4.2 16.4 - - + -
547A MET* 3.5 26.6 - - + +
558A ILE 4.3 0.2 - - - -
559A VAL* 1.3 75.5 - - - +
561A GLN* 1.3 64.1 + - - +
562A SER* 3.4 18.6 - - - -
572A LEU* 3.3 20.5 - - + +
594A GLN* 3.5 16.6 + - - +
596A LEU* 4.5 2.9 - - + -
610A TYR* 3.5 40.4 - + + -
611A LYS 3.5 8.7 - - - -
612A LEU* 3.9 17.5 - - + -
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Residues in contact with GLN 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A VAL* 3.7 24.5 - - + +
560A PHE* 1.3 78.2 - - - +
562A SER* 1.3 69.1 + - - +
572A LEU* 3.9 7.4 - - + -
610A TYR* 3.2 4.7 - - - +
611A LYS* 2.9 65.5 + - + +
613A THR* 4.6 9.3 + - - -
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Residues in contact with SER 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A PHE* 3.4 17.7 - - - -
561A GLN* 1.3 81.9 + - - +
563A ALA* 1.3 60.8 + - - +
570A VAL* 3.9 15.3 - - - +
572A LEU* 4.1 21.4 - - - +
596A LEU* 4.3 4.4 - - - +
608A LEU* 3.3 33.4 - - - +
609A ARG 3.3 6.3 - - - -
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Residues in contact with ALA 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A SER* 1.3 74.7 - - - +
564A VAL* 1.3 65.0 + - - +
570A VAL* 4.6 3.4 - - - -
607A ARG 4.4 0.2 - - - +
608A LEU* 3.7 6.6 - - - +
609A ARG* 2.7 42.7 + - + +
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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