Contacts of the strand formed by residues 2568 - 2573 (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 PHE2568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2490A ALA* 4.2 18.4 - - + -
2495A LEU* 3.6 49.4 - - + +
2551A TYR 3.5 0.9 - - - +
2552A LEU* 3.4 5.6 - - - -
2553A ILE* 2.8 49.0 + - + +
2555A ILE* 3.8 23.3 - - + -
2563A ILE* 4.2 3.8 - - + -
2564A VAL 3.7 12.6 - - - -
2565A GLY* 3.3 35.4 - - - -
2566A SER* 3.7 9.6 - - - -
2567A PRO* 1.3 72.3 - - - +
2569A LYS* 1.3 60.9 + - - +
2570A ALA 3.9 0.4 + - - -
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Residues in contact with LYS2569 (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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2495A LEU 3.4 9.6 - - - +
2496A GLU* 4.0 6.2 - - - +
2550A ASN* 4.0 40.4 - - + +
2551A TYR 3.4 8.1 - - - +
2552A LEU* 4.2 20.2 - - + -
2567A PRO 3.9 2.0 + - - +
2568A PHE* 1.3 72.5 - - - +
2570A ALA* 1.3 63.7 + - - +
2571A LYS* 4.1 0.8 + - + -
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Residues in contact with ALA2570 (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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2494A GLY 3.9 2.5 - - - +
2495A LEU 3.8 7.2 - - - +
2496A GLU 3.4 6.1 - - - -
2497A GLY* 3.7 18.4 - - - +
2543A TYR* 3.7 19.7 - - - +
2549A GLY 3.6 1.2 - - - +
2550A ASN* 3.4 4.3 - - - -
2551A TYR* 2.8 41.2 + - + +
2553A ILE* 4.0 9.2 - - + -
2568A PHE 3.9 1.0 + - - -
2569A LYS* 1.3 75.5 - - - +
2571A LYS* 1.3 60.2 + - - +
2572A VAL* 4.9 2.0 - - + -
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Residues in contact with LYS2571 (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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2496A GLU 3.0 11.5 + - - +
2497A GLY* 3.0 20.3 - - - -
2498A GLY 3.2 3.6 + - - +
2549A GLY* 3.5 22.5 - - - +
2550A ASN* 2.6 38.3 + - - +
2569A LYS* 4.1 1.5 + - + -
2570A ALA* 1.3 71.7 - - - +
2572A VAL* 1.3 68.6 + - - +
2573A THR* 5.1 10.7 - - + +
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Residues in contact with VAL2572 (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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2497A GLY 4.6 2.2 - - - -
2498A GLY* 3.2 17.7 - - - +
2500A THR* 3.8 18.4 - - + +
2543A TYR* 5.0 6.3 - - - +
2545A PRO* 3.7 30.1 - - + -
2547A ALA 3.8 5.8 - - - +
2548A PRO* 3.3 3.0 - - - +
2549A GLY 2.9 29.1 + - - +
2551A TYR* 3.6 33.7 - - + -
2570A ALA* 4.7 3.1 - - + +
2571A LYS* 1.3 82.7 - - - +
2573A THR* 1.3 77.1 + - - +
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Residues in contact with THR2573 (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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2498A GLY 3.1 5.3 + - - +
2499A THR* 3.1 23.3 - - - +
2500A THR* 2.9 28.9 + - - +
2548A PRO* 4.3 3.1 - - - -
2571A LYS* 5.1 12.3 - - + +
2572A VAL* 1.3 77.2 - - - +
2574A GLY* 1.3 62.1 + - - +
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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