Contacts of the strand formed by residues 17 - 25 (chain C) in PDB entry 2VWI
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 TYR 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C TRP* 3.7 17.3 - - - -
11C SER* 2.6 38.1 + - - -
13C ASN 3.3 21.1 - - - -
14C ARG* 3.1 32.6 + - - +
15C ASP* 3.4 0.4 - - - -
16C ASP* 1.3 80.8 - - + +
18C GLU* 1.3 61.2 + - - +
19C LEU* 3.8 0.9 - - + -
34C ALA* 4.5 4.0 - - + -
35C TYR 3.3 4.3 - - - +
36C CYS* 3.6 32.5 - - + -
43C VAL* 4.2 6.1 - - + -
45C ILE* 4.1 24.7 - - + -
80C THR* 3.8 7.6 - - - +
82C PHE* 3.8 21.1 - + - -
89C TRP* 5.0 3.8 - - + -
91C VAL* 3.9 21.1 - - + -
254D LYS* 3.6 6.7 - - - -
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 1.3 70.7 - - - +
19C LEU* 1.3 69.3 + - - +
20C GLN* 3.4 26.1 + - - +
34C ALA* 3.2 3.6 - - - -
35C TYR* 2.8 39.9 + - + +
252D GLN 3.3 19.7 - - - +
253D ASP* 3.6 10.6 - - - +
254D LYS* 2.8 50.2 + - + +
255D GLU* 4.0 9.4 + - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG* 3.4 31.3 - - - +
17C TYR* 3.6 3.1 + - + +
18C GLU* 1.3 78.2 - - - +
20C GLN* 1.3 62.3 - - - +
32C GLN* 3.7 32.8 - - + +
33C ALA 3.9 1.3 - - - -
34C ALA* 4.3 13.5 - - + -
45C ILE* 4.4 5.4 - - + -
47C ARG* 3.5 27.1 - - - +
89C TRP* 4.0 25.1 - - + -
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASN* 4.5 1.2 - - - +
18C GLU* 3.7 19.4 + - - +
19C LEU* 1.3 77.7 - - - +
21C GLU* 1.3 74.7 + - - +
22C VAL 3.6 0.3 + - - -
32C GLN* 2.9 23.4 + - - -
33C ALA 2.8 14.4 + - - +
34C ALA* 3.8 5.4 - - - -
35C TYR* 3.7 28.7 + - - +
42C LYS* 2.9 28.4 + - - +
255D GLU* 2.8 28.9 + - - -
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A TYR* 4.2 14.8 - - + +
230A TYR* 2.6 37.9 + - + +
238A LEU* 3.9 15.3 - - + -
242A ASN* 3.5 20.6 - - - +
20C GLN* 1.3 88.5 - - - +
22C VAL* 1.3 60.2 + - - +
23C ILE* 3.5 0.7 + - + -
32C GLN* 4.0 0.4 - - - -
33C ALA* 2.8 31.0 + - - +
42C LYS* 2.8 25.2 + - - -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LEU* 3.4 11.5 - - - +
241A GLN* 3.9 30.7 - - + +
242A ASN* 2.8 33.4 + - - +
21C GLU* 1.3 69.6 - - - +
23C ILE* 1.3 64.0 + - - +
24C GLY 3.5 26.0 - - - +
25C SER* 4.3 3.8 - - - -
30C VAL* 3.8 16.4 - - + -
31C VAL 3.7 3.4 - - - +
32C GLN* 3.8 28.7 - - + +
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TYR* 3.7 43.7 - - + +
234A LYS* 2.8 40.9 + - - -
237A MET* 4.3 9.7 - - - +
238A LEU* 4.1 7.6 - - + +
241A GLN* 5.8 1.0 - - - +
21C GLU 4.1 5.8 - - - +
22C VAL* 1.3 77.1 - - - +
24C GLY* 1.3 51.6 + - - +
31C VAL* 2.7 27.4 + - + +
32C GLN 4.4 0.2 - - - -
33C ALA* 3.9 20.2 - - + +
44C ALA* 4.9 2.5 - - + -
94C LEU* 4.4 13.9 - - + -
1294C ANP 3.5 34.8 - - + +
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LYS* 4.3 2.7 - - - -
237A MET* 5.9 2.0 - - - -
241A GLN* 5.4 1.3 - - - -
22C VAL* 3.5 2.7 - - - +
23C ILE* 1.3 79.3 - - - +
25C SER* 1.3 60.9 + - - -
26C GLY 4.2 0.7 - - - -
29C ALA 4.6 0.4 - - - -
30C VAL* 3.3 10.3 - - - +
31C VAL* 2.8 30.2 + - - +
1294C ANP 3.8 24.5 - - - -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 3.4 40.0 + - - +
22C VAL* 4.3 5.6 - - - -
24C GLY* 1.3 75.5 - - - -
26C GLY* 1.3 62.9 + - - +
29C ALA 3.8 3.6 - - - -
30C VAL* 4.4 9.0 - - - +
1294C ANP 5.1 0.6 - - - -
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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