Contacts of the strand formed by residues 2549 - 2557 (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 GLY2549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2525A PRO* 4.1 4.3 - - - -
2547A ALA 4.0 0.2 + - - -
2548A PRO* 1.3 75.8 - - - +
2550A ASN* 1.3 61.3 + - - -
2551A TYR* 3.7 7.9 - - - -
2570A ALA 3.6 0.9 - - - +
2571A LYS* 3.5 19.9 - - - +
2572A VAL 2.9 33.5 + - - -
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Residues in contact with ASN2550 (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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2523A ASP 4.1 0.5 - - - +
2524A GLY* 3.7 4.5 - - - -
2525A PRO* 3.5 17.5 - - - +
2549A GLY* 1.3 71.6 - - - -
2551A TYR* 1.3 60.0 + - - +
2552A LEU* 4.3 1.6 + - + +
2569A LYS* 4.0 42.0 - - + +
2570A ALA 3.4 3.4 - - - -
2571A LYS* 2.6 40.4 + - - +
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Residues in contact with TYR2551 (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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2522A ILE* 4.0 25.6 - - + -
2523A ASP 3.2 4.3 - - - +
2524A GLY* 3.8 10.1 - - - -
2525A PRO* 3.6 17.7 - - + -
2526A SER* 2.7 45.5 + - - -
2528A VAL* 3.8 11.7 - - + -
2543A TYR* 5.4 3.8 - + + -
2545A PRO* 3.8 7.6 - - + +
2547A ALA* 2.5 33.7 + - - +
2549A GLY 3.7 6.1 - - - -
2550A ASN* 1.3 76.0 - - - +
2552A LEU* 1.3 63.4 + - - +
2553A ILE* 4.0 2.2 - - + -
2568A PHE 3.5 0.9 - - - +
2569A LYS* 3.4 5.8 - - - +
2570A ALA* 2.8 42.3 + - + +
2572A VAL* 3.6 30.5 - - + -
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Residues in contact with LEU2552 (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* 3.6 1.9 + - - +
2522A ILE* 3.4 2.4 - - - -
2523A ASP* 2.7 44.6 + - + +
2550A ASN* 4.2 1.7 - - + +
2551A TYR* 1.3 73.0 - - - +
2553A ILE* 1.3 61.3 + - - +
2554A ALA* 3.9 2.4 + - + +
2567A PRO* 4.1 26.9 - - + +
2568A PHE 3.4 12.6 - - - +
2569A LYS* 4.2 28.3 - - + -
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Residues in contact with ILE2553 (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 3.5 24.5 - - - +
2495A LEU* 4.1 15.5 - - + +
2506A PHE* 3.8 29.8 - - + -
2520A VAL* 4.4 2.0 - - + -
2521A THR 3.3 9.0 - - - +
2522A ILE* 4.0 21.1 - - + -
2543A TYR* 3.9 14.1 - - + +
2551A TYR* 4.6 3.6 - - + +
2552A LEU* 1.3 74.6 - - - +
2554A ALA* 1.3 61.1 + - - +
2555A ILE* 4.1 15.0 - - + -
2567A PRO* 3.4 2.6 - - - +
2568A PHE* 2.8 45.8 + - + +
2570A ALA* 4.0 12.8 - - + -
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Residues in contact with ALA2554 (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* 3.5 2.6 + - - +
2520A VAL* 3.3 5.2 - - - -
2521A THR* 2.9 46.9 + - - +
2523A ASP* 6.1 0.2 - - - +
2552A LEU* 3.9 2.5 - - + +
2553A ILE* 1.3 72.7 - - - +
2555A ILE* 1.3 61.6 + - - +
2556A LYS* 4.1 11.2 - - - +
2562A HIS* 3.8 21.8 - - + -
2566A SER* 3.4 5.2 - - - -
2567A PRO* 4.3 5.8 - - + -
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Residues in contact with ILE2555 (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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2490A ALA* 4.2 7.2 - - + -
2495A LEU* 4.2 1.3 - - + -
2506A PHE* 3.8 27.4 - - + -
2508A VAL* 4.1 13.9 - - + -
2518A LEU* 3.7 26.0 - - + -
2519A SER 3.3 4.5 - - - +
2520A VAL* 4.4 9.4 - - + -
2553A ILE* 4.1 13.9 - - + +
2554A ALA* 1.3 77.2 - - - +
2556A LYS* 1.3 60.8 + - - +
2562A HIS* 3.5 1.9 - - - -
2563A ILE* 2.9 46.3 + - + +
2566A SER* 2.9 15.1 + - - +
2568A PHE* 3.8 24.7 - - + -
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Residues in contact with LYS2556 (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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2517A ALA 4.5 0.2 - - - -
2518A LEU* 3.5 6.8 - - - +
2519A SER* 2.9 48.7 + - - +
2554A ALA* 4.7 8.5 - - + -
2555A ILE* 1.3 79.7 - - - +
2557A TYR* 1.3 61.3 + - - +
2559A GLY 3.8 12.1 - - - +
2560A PRO* 3.7 24.4 + - + +
2561A GLN 3.2 17.9 - - - +
2562A HIS* 3.8 30.7 + - + +
2563A ILE* 4.4 2.0 - - - -
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Residues in contact with TYR2557 (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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2483A GLY* 4.2 2.2 - - - -
2484A ASP 4.1 16.2 - - - -
2485A PRO* 3.7 28.1 - - + +
2488A VAL* 3.6 23.6 - - + -
2510A THR* 3.7 32.4 + - + -
2513A ALA* 3.4 25.6 - - + -
2514A GLY 2.8 21.8 + - - -
2515A SER* 3.9 0.3 - - - -
2516A GLY* 3.2 37.5 + - - -
2517A ALA 3.4 11.0 - - - -
2518A LEU* 3.9 20.0 - - + -
2539A HIS* 5.8 0.4 - - - -
2556A LYS* 1.3 77.3 - - - +
2558A GLY* 1.3 65.1 + - - +
2559A GLY* 3.3 5.4 + - - +
2561A GLN* 3.2 9.5 + - - +
2563A ILE* 4.1 5.3 - - + +
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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