Contacts of the strand formed by residues 2518 - 2523 (chain A) in PDB entry 2NQC
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 LEU2518 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A IMD 3.2 38.5 + - + +
2488A VAL* 4.9 1.6 - - + -
2508A VAL* 3.8 20.6 - - + -
2510A THR* 4.3 2.0 - - + -
2516A GLY 3.8 2.6 + - - -
2517A ALA* 1.3 75.0 - - - +
2519A SER* 1.3 59.7 + - - +
2520A VAL* 4.2 10.8 - - + -
2539A HIS* 3.6 44.2 - - + +
2555A ILE* 3.7 22.9 - - + -
2556A LYS 3.5 15.9 - - - +
2557A TYR* 3.9 22.0 - - + -
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Residues in contact with SER2519 (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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201A IMD 4.7 0.4 - - - -
2517A ALA 3.9 1.1 + - - -
2518A LEU* 1.3 75.0 - - - +
2520A VAL* 1.3 64.3 + - - +
2521A THR* 4.3 13.3 + - - +
2554A ALA 3.5 1.6 + - - +
2555A ILE* 3.3 6.4 - - - +
2556A LYS* 2.9 55.4 + - - +
2559A GLY 5.7 1.3 - - - -
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Residues in contact with VAL2520 (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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201A IMD 4.2 27.3 - - + -
2506A PHE* 4.2 22.4 - - + -
2508A VAL* 4.9 2.9 - - + -
2518A LEU* 4.2 13.2 + - + -
2519A SER* 1.3 79.2 + - - +
2521A THR* 1.3 68.7 + - - +
2522A ILE* 4.5 1.3 - - + -
2530A LEU* 3.8 30.6 - - + +
2541A VAL* 4.5 13.2 - - + -
2553A ILE* 4.4 9.4 - - + -
2554A ALA 3.3 6.5 - - - +
2555A ILE* 4.4 12.3 - - + -
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Residues in contact with THR2521 (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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2519A SER* 4.3 12.1 - - - +
2520A VAL* 1.3 77.1 - - - +
2522A ILE* 1.3 66.2 + - - +
2523A ASP* 4.2 15.9 + - - -
2530A LEU* 4.8 2.2 - - - -
2552A LEU 3.6 1.0 + - - +
2553A ILE* 3.3 5.0 - - - +
2554A ALA* 2.9 51.3 + - - +
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Residues in contact with ILE2522 (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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401A GOL 5.3 4.3 + - - -
2506A PHE* 4.6 2.9 - - + -
2520A VAL* 4.5 2.0 - - + -
2521A THR* 1.3 80.3 - - - +
2523A ASP* 1.3 69.9 + - - +
2524A GLY 4.4 0.3 + - - -
2527A LYS* 5.9 1.2 - - - -
2528A VAL* 3.7 28.2 + - + +
2530A LEU* 3.8 27.6 - - + +
2543A TYR* 3.6 42.8 - - + -
2551A TYR* 4.0 23.6 - - + -
2552A LEU 3.4 6.3 - - - +
2553A ILE* 4.0 26.5 - - + -
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Residues in contact with ASP2523 (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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2521A THR* 4.2 15.2 + - - -
2522A ILE* 1.3 84.6 + - - +
2524A GLY* 1.3 58.3 + - - +
2526A SER 5.6 0.2 - - - -
2550A ASN 4.1 0.5 - - - +
2551A TYR* 3.2 5.5 - - - -
2552A LEU* 2.7 48.7 + - + +
2554A ALA* 6.1 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