Contacts of the strand formed by residues 19 - 29 (chain X) in PDB entry 5A0Q
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 VAL 19 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13X MET 4.0 4.5 - - - +
14X LYS* 4.4 2.7 - - + +
17X ASN 3.3 15.3 - - - +
18X CYS* 1.4 68.2 - - - +
20X ALA* 1.3 61.3 + - - +
21X ILE* 4.6 1.0 - - - +
109X ALA* 4.0 4.7 - - + -
110X GLY* 3.8 25.6 - - - +
111X LEU* 3.4 17.7 - - + -
118X PRO* 3.4 26.2 - - + -
120X ILE* 3.4 32.8 - - + -
187X HIS 3.4 2.6 - - - +
188X ILE* 4.2 0.9 - - - -
189X ILE* 2.9 35.3 + - + +
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Residues in contact with ALA 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ALA* 3.8 0.5 - - - -
13X MET* 2.8 40.0 + - + +
19X VAL* 1.3 72.5 - - - +
21X ILE* 1.4 64.0 + - - +
109X ALA* 4.1 6.4 - - - +
162X LEU* 3.5 27.7 - - + +
166X ILE* 3.5 23.3 - - + -
187X HIS 3.5 5.8 - - - -
188X ILE* 4.2 12.1 - - + +
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Residues in contact with ILE 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 5.0 3.6 - - + -
11X MET 3.3 16.2 - - - +
12X ALA* 4.0 5.8 - - + +
19X VAL 4.6 2.2 - - - +
20X ALA* 1.4 77.8 - - - +
22X ALA* 1.4 66.5 + - - +
41X ILE* 4.1 24.4 - - + +
49X TYR* 4.9 9.0 - - + -
50X ILE* 4.3 2.9 - - - +
51X GLY* 4.0 16.2 - - - +
107X VAL 3.6 24.7 - - - +
109X ALA* 3.9 24.0 - - + +
166X ILE* 3.6 4.7 - - - -
186X VAL* 3.5 2.8 - - - +
187X HIS* 2.9 48.5 + - + +
189X ILE* 5.0 1.3 - - + -
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Residues in contact with ALA 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 3.8 2.4 - - - +
11X MET* 3.0 39.6 + - + +
21X ILE* 1.4 77.1 - - - +
23X ALA* 1.3 64.2 + - - +
41X ILE* 3.8 5.8 - - - +
166X ILE* 3.7 19.4 - - + +
170X MET* 4.6 11.2 - - + -
184X VAL* 4.9 0.2 - - + -
185X ILE 3.0 15.7 - - - +
186X VAL* 3.9 14.1 - - + -
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Residues in contact with ALA 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ALA 3.7 16.2 - - - +
10X VAL* 4.8 3.8 - - + -
22X ALA* 1.3 80.8 - - - +
24X ASP* 1.4 68.1 + - - +
40X LYS* 4.3 13.5 - - + -
41X ILE* 3.9 21.5 - - + +
51X GLY* 6.3 0.2 - - - -
170X MET* 3.6 11.4 - - - -
184X VAL* 3.6 1.9 - - - -
185X ILE* 3.1 34.9 + - + +
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Residues in contact with ASP 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X GLY* 3.6 9.5 - - - -
9X ALA* 2.9 34.4 + - + +
23X ALA* 1.4 73.5 - - - +
25X ARG* 1.3 61.3 + - - +
26X ARG* 3.5 18.8 + - - +
38X PHE 4.3 1.0 - - - +
40X LYS* 3.7 18.4 - - - +
170X MET* 3.3 16.9 - - + +
179X VAL 4.5 0.7 - - - +
180X SER* 3.5 24.5 + - - -
181X GLY 3.6 20.9 + - - +
183X GLY 3.4 9.0 - - - +
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Residues in contact with ARG 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X ALA 4.6 0.7 - - - +
24X ASP* 1.3 73.7 - - - +
26X ARG* 1.3 59.0 - - - +
36X THR* 2.8 46.0 + - - +
37X ASP* 4.0 25.3 + - - +
38X PHE 3.9 26.0 - - - +
39X GLN* 5.5 1.8 - - - -
40X LYS 6.0 0.7 - - - +
181X GLY 4.3 0.4 + - - -
182X MET 3.0 14.2 - - - +
183X GLY* 3.1 36.5 + - - +
184X VAL 3.4 12.8 + - - +
185X ILE* 4.1 34.5 - - + -
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Residues in contact with ARG 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG 4.1 3.4 + - - -
168L ALA* 4.1 14.6 - - - +
7X GLY 4.6 1.7 - - - +
8X GLY* 4.9 0.2 - - - -
24X ASP* 3.5 12.1 - - - +
25X ARG* 1.3 78.1 - - - +
27X PHE* 1.3 71.7 + - - +
28X GLY* 4.6 6.1 - - - -
30X GLN 5.7 0.2 + - - -
31X ALA 4.0 10.7 + - - -
32X GLN 3.9 4.4 + - - -
33X MET* 1.4 93.9 - - + +
35X THR 3.4 10.5 - - - +
38X PHE* 4.4 5.7 - - - +
40X LYS* 3.5 19.2 - - - -
178X ALA 5.1 1.6 + - - -
179X VAL* 4.3 22.8 + - - +
180X SER* 5.2 1.5 - - - -
181X GLY 3.3 20.2 - - - +
182X MET* 3.1 31.8 - - + +
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Residues in contact with PHE 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ASN* 3.6 18.4 - - - +
7X GLY 4.7 7.4 - - - +
26X ARG* 1.3 84.5 - - - +
28X GLY* 1.3 63.0 + - - +
29X ILE* 5.9 0.2 - - + -
34X VAL* 3.1 56.3 + - + +
35X THR* 2.4 31.5 + - - -
38X PHE* 3.1 51.6 - + + -
40X LYS* 4.8 0.2 - - - +
56X ALA* 5.2 6.1 - - + -
179X VAL 5.7 2.9 - - - -
117Y TYR* 4.7 7.6 - + - -
119Y ASP* 6.0 1.3 - - - -
123Y ALA* 4.7 13.9 - - + -
125Y ALA* 3.5 21.3 - - + -
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Residues in contact with GLY 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ASN* 3.0 33.0 + - - +
26X ARG* 4.6 5.8 - - - +
27X PHE* 1.3 79.1 - - - +
29X ILE* 1.3 62.7 + - - -
30X GLN 3.4 12.0 + - - +
32X GLN 3.3 15.3 - - - -
33X MET* 4.3 1.1 - - - -
34X VAL* 4.0 1.6 - - - -
179X VAL 5.6 1.8 + - - -
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Residues in contact with ILE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X PHE* 5.9 0.4 - - + -
28X GLY* 1.3 67.4 - - - -
30X GLN* 1.3 73.7 + - + +
32X GLN* 3.0 36.7 + - + +
34X VAL* 3.3 22.6 - - + +
117Y TYR* 3.6 18.6 - - + +
119Y ASP* 3.1 37.9 - - - +
120Y TYR* 4.7 12.3 - - + +
121Y LEU* 5.9 1.3 - - + -
137Y PHE* 5.3 6.8 - - + -
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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