Contacts of the strand formed by residues 49 - 58 (chain A) in PDB entry 1QRW
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 ALA 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA* 6.5 0.4 - - + -
45A ARG* 3.1 4.1 - - - -
46A ILE 2.9 32.9 + - - +
47A GLY 3.2 3.3 - - - +
48A GLY* 1.3 80.1 - - - +
50A VAL* 1.3 68.7 + - - +
51A VAL* 3.4 4.3 + - + +
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Residues in contact with VAL 50 (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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43A THR* 3.8 26.2 - - + -
44A ALA 3.5 5.2 - - - -
45A ARG* 3.8 28.0 - - - +
48A GLY 4.3 0.4 + - - -
49A ALA* 1.3 76.1 - - - +
51A VAL* 1.3 63.8 + - - +
52A GLY* 3.9 12.3 - - - +
53A THR* 5.7 1.1 - - + -
70A THR* 5.1 8.1 - - + +
73A GLN* 4.1 6.8 + - - -
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Residues in contact with VAL 51 (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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1A ALA* 4.0 8.3 - - + +
3A ILE* 5.2 0.4 - - + -
31A PHE* 4.8 1.6 - - + -
44A ALA* 2.9 30.8 + - + +
46A ILE* 3.9 35.7 - - + +
49A ALA* 3.6 12.3 - - + +
50A VAL* 1.3 78.4 - - - +
52A GLY* 1.3 59.0 + - - +
69A LEU* 3.3 24.4 - - + +
70A THR* 3.0 28.5 + - - +
73A GLN* 3.3 32.7 - - - +
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Residues in contact with GLY 52 (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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43A THR* 3.7 4.2 - - - +
44A ALA* 2.9 23.6 + - - +
50A VAL* 3.7 6.6 - - - +
51A VAL* 1.3 84.5 - - - +
53A THR* 1.3 69.7 + - - +
67A VAL* 4.1 7.0 - - - -
68A SER 3.2 13.7 - - - -
69A LEU* 4.1 1.6 - - - -
70A THR* 4.5 6.1 - - - -
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Residues in contact with THR 53 (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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41A ASN* 4.0 20.3 + - - +
42A ALA 3.1 13.0 - - - +
43A THR* 4.3 11.2 - - + +
44A ALA 4.5 0.4 - - - +
50A VAL* 5.7 2.2 - - + -
52A GLY* 1.3 80.4 - - - +
54A PHE* 1.3 67.5 + - - +
55A ALA* 5.3 0.3 - - - -
67A VAL* 3.8 6.7 - - - +
68A SER* 2.8 42.0 + - - -
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Residues in contact with PHE 54 (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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9A TYR* 3.5 27.4 - + - -
11A ILE* 3.8 23.8 - - + -
33A THR* 3.9 17.0 - - + -
34A ALA 4.2 1.8 - - - -
37A CYS 3.9 3.1 - - - -
38A GLY* 3.7 37.0 - - - -
39A THR 3.3 22.0 - - - +
40A VAL* 3.9 2.8 - - - +
41A ASN* 2.8 29.8 + - - +
42A ALA* 2.9 26.2 + - + +
44A ALA* 4.8 5.4 - - + -
53A THR* 1.3 72.3 + - - +
55A ALA* 1.3 63.2 + - - +
56A ALA 3.5 3.4 - - - +
57A ARG* 5.0 0.4 - - + -
65A ALA* 4.0 19.5 - - + -
66A TRP 3.8 4.7 - - - -
67A VAL* 3.8 17.7 - - + +
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Residues in contact with ALA 55 (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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40A VAL* 3.8 13.4 - - - +
41A ASN* 6.0 0.2 - - - +
53A THR* 3.2 2.9 + - - -
54A PHE* 1.3 73.3 - - - +
56A ALA* 1.3 64.7 + - - +
66A TRP* 2.9 46.5 + - + +
68A SER* 3.8 18.4 - - - +
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Residues in contact with ALA 56 (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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40A VAL* 4.1 10.1 - - - -
54A PHE* 3.5 3.6 - - - -
55A ALA* 1.3 81.8 - - - +
57A ARG* 1.3 66.9 + - - +
65A ALA* 3.3 2.3 - - - +
66A TRP* 3.2 32.1 + - - +
191A TYR* 3.4 32.8 - - + +
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Residues in contact with ARG 57 (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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35A GLY* 3.0 30.2 + - - -
36A HIS* 4.0 10.7 + - - +
38A GLY 3.0 25.0 + - - +
39A THR* 4.2 19.7 - - - +
40A VAL* 4.0 23.5 - - + +
54A PHE* 5.0 1.1 - - + -
56A ALA* 1.3 82.0 - - - +
58A VAL* 1.3 71.3 + - - +
59A PHE* 3.7 31.0 + - - +
64A ARG 3.2 13.7 - - - +
65A ALA* 3.5 9.9 - - + -
191A TYR* 3.4 3.4 + - - -
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Residues in contact with VAL 58 (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 ARG* 1.3 79.0 - - - +
59A PHE* 1.3 63.6 + - - +
60A PRO 3.9 9.0 - - - +
61A GLY* 5.4 0.2 - - - -
62A ASN* 3.2 33.7 - - + +
64A ARG* 2.9 42.6 + - + -
190A GLN* 4.4 19.3 - - - +
191A TYR* 3.4 14.4 - - - +
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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