Contacts of the strand formed by residues 492 - 503 (chain A) in PDB entry 2NUP
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 ARG 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.7 3.3 - - - +
121A VAL* 3.2 49.8 + - + +
124A GLY 6.2 0.2 - - - +
126A GLN* 5.9 4.0 - - + -
281A ASN 5.8 2.0 + - - -
403A GLY 5.0 8.7 + - - -
485A TYR* 3.8 8.6 + - - +
486A GLN* 4.8 24.7 + - - +
490A GLY 4.4 6.3 - - - +
491A GLN* 1.3 74.9 - - - +
493A ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 493 (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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53A PRO* 6.1 4.3 - - - +
118A GLU* 3.2 33.7 + - - +
119A TYR 3.5 10.8 - - - +
120A VAL* 4.4 12.5 - - + +
397A GLN* 5.2 1.8 + - - -
483A THR 3.5 0.9 - - - +
484A GLN* 3.3 4.7 - - - +
485A TYR* 3.0 53.6 + - + +
487A HIS* 3.1 44.9 + - + +
489A SER* 4.5 1.6 + - - -
491A GLN* 3.4 30.5 + - + +
492A ARG* 1.3 81.5 - - - +
494A ILE* 1.3 67.0 + - - +
495A ARG 4.1 0.7 - - - -
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Residues in contact with ILE 494 (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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57A GLU* 5.3 2.0 - - - +
58A PRO* 4.6 17.5 - - + -
118A GLU* 3.4 3.5 - - - -
119A TYR* 2.9 49.7 + - + +
121A VAL* 3.8 25.8 - - + -
482A VAL* 4.0 20.2 - - + -
483A THR 3.2 3.6 - - - +
484A GLN* 3.8 27.6 - - + +
492A ARG* 6.5 0.2 - - + -
493A ARG* 1.3 79.5 - - - +
495A ARG* 1.3 62.0 + - - +
496A VAL* 3.7 20.4 - - + -
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Residues in contact with ARG 495 (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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44A PRO 2.4 38.7 + - - +
45A LEU* 2.7 29.7 + - + +
46A LYS 2.7 28.1 + - - +
48A ARG* 5.1 8.9 - - - +
51A LEU* 6.1 3.4 - - - +
116A SER* 5.9 3.9 + - - +
117A ILE* 3.8 4.9 - - - +
118A GLU* 2.9 46.3 + - - +
481A PHE 3.6 1.3 - - - +
482A VAL* 3.5 2.3 - - - -
483A THR* 2.7 51.9 + - - +
485A TYR* 4.6 0.6 - - + -
493A ARG 4.1 0.6 - - - -
494A ILE* 1.3 73.7 - - - +
496A VAL* 1.3 66.5 + - - +
497A THR* 5.4 4.3 - - - +
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 4.2 22.7 - - + -
70A LEU 5.8 1.3 - - - +
71A ASN* 6.0 1.1 - - + -
116A SER* 2.7 10.8 + - - +
117A ILE* 2.6 47.8 + - + +
119A TYR* 3.4 27.8 - - + +
480A GLN* 4.2 24.0 - - + +
481A PHE 3.4 5.8 - - - +
482A VAL* 4.4 4.0 - - + -
494A ILE* 3.7 16.4 - - + -
495A ARG* 1.3 81.2 - - - +
497A THR* 1.3 58.0 + - - +
498A THR* 4.2 7.0 - - - +
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Residues in contact with THR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.1 45.2 + - + +
17A VAL* 5.7 0.4 - - + -
42A PHE* 4.6 9.0 - - + -
44A PRO 5.6 1.7 + - - -
116A SER* 2.8 23.1 + - - +
480A GLN* 3.4 1.9 - - - +
481A PHE* 2.7 56.3 + - + +
495A ARG* 5.4 4.7 - - - +
496A VAL* 1.3 74.4 - - - +
498A THR* 1.3 61.7 + - - +
499A ILE* 3.8 12.3 - - + -
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Residues in contact with THR 498 (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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15A ASP* 4.8 0.9 - - - +
71A ASN* 3.6 29.9 - - - +
72A PRO* 5.2 3.7 - - - +
73A LEU* 3.8 30.7 - - + +
87A PHE* 4.6 5.2 - - + -
115A SER* 4.0 18.5 - - - -
116A SER 4.1 6.6 - - - +
479A ILE 3.5 10.1 - - - +
480A GLN* 3.1 32.7 + - + +
496A VAL* 4.2 4.9 - - - +
497A THR* 1.3 72.4 - - - +
499A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 499 (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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15A ASP* 4.0 19.3 - - + +
17A VAL* 4.0 14.8 - - + -
19A PHE* 3.3 36.1 - - + -
24A TRP* 3.9 10.8 - - + -
478A ALA* 3.6 5.0 - - - +
479A ILE* 3.1 43.4 + - + +
481A PHE* 4.4 6.3 - - + -
497A THR* 3.8 21.5 - - + -
498A THR* 1.3 80.2 - - - +
500A ALA* 1.3 67.4 + - - +
501A ARG* 3.8 29.2 - - + +
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Residues in contact with ALA 500 (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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73A LEU* 3.8 32.3 - - + -
476A ARG* 2.6 42.2 + - + +
477A GLY 3.3 11.0 - - - +
478A ALA* 4.7 0.4 - - + -
499A ILE* 1.3 78.7 - - - +
501A ARG* 1.3 70.8 + - - +
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Residues in contact with ARG 501 (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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7A PHE* 4.3 14.3 - - - -
11A ASN* 3.5 32.4 - - - +
17A VAL* 4.0 14.1 + - - +
19A PHE* 3.9 22.1 - - + -
21A TRP 4.9 0.2 - - - +
22A ASN* 3.2 46.8 + - - +
24A TRP* 3.3 44.5 - - + -
476A ARG* 3.0 5.3 - - - +
477A GLY 2.6 37.7 + - - -
499A ILE* 3.8 14.6 - - + +
500A ALA* 1.3 102.2 + - - +
502A ASN* 1.3 62.0 + - - +
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Residues in contact with ASN 502 (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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22A ASN 3.8 4.4 + - - -
23A VAL* 3.3 20.5 - - + +
24A TRP* 3.1 23.9 + - - +
474A GLY 5.3 1.9 - - - +
475A GLY* 5.0 2.6 - - - -
476A ARG* 3.1 45.9 + - - +
501A ARG* 1.3 73.5 - - - +
503A TRP* 1.3 66.5 + - - +
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Residues in contact with TRP 503 (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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23A VAL* 4.6 0.4 - - - +
24A TRP* 3.8 25.6 - + + -
25A PRO 3.4 27.4 - - - -
26A SER* 4.1 10.1 - - - -
413A GLU* 3.0 44.4 + - + -
414A ILE* 3.5 23.6 - - + -
463A VAL* 4.2 11.4 - - + -
475A GLY* 3.4 21.1 - - - -
476A ARG 3.2 41.1 + - - +
477A GLY* 3.6 17.0 - - - -
502A ASN* 1.3 77.0 - - - +
504A ALA* 1.3 69.9 + - - +
505A ASP* 3.5 8.7 + - - +
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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