Contacts of the strand formed by residues 31 - 38 (chain O) in PDB entry 2V10
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 GLN 31 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ILE 2.9 32.5 + - - +
29O PRO* 3.4 17.2 + - - +
30O PRO* 1.4 67.9 - - - +
32O THR* 1.4 59.5 + - - +
33O PHE* 3.3 25.0 - - + -
62O LYS* 4.2 16.2 - - - +
63O LEU 4.8 2.0 + - - +
64O PHE* 3.5 14.8 - - + -
65O ASP* 3.3 44.8 + - - +
68O ASP* 3.2 25.9 + - - +
69O SER* 4.6 2.1 - - - -
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Residues in contact with THR 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASP* 4.0 19.6 + - - +
276C GLU 5.9 0.9 - - - +
278C THR* 4.0 27.3 - - + +
23O GLU* 4.0 16.9 + - - -
24O ILE 3.1 15.7 - - - +
25O GLY* 4.2 1.6 - - - -
30O PRO* 4.0 20.9 - - + +
31O GLN* 1.4 72.6 - - - +
33O PHE* 1.4 56.9 + - - +
62O LYS* 3.2 27.5 + - - +
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Residues in contact with PHE 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASP* 5.8 0.2 - - - -
23O GLU* 3.2 12.3 - - - +
24O ILE* 3.0 33.4 + - + +
26O ILE* 3.8 23.1 - - + -
31O GLN* 3.3 30.1 - - + -
32O THR* 1.4 68.7 + - - +
34O LYS* 1.4 65.1 - - - +
35O VAL* 3.9 4.6 + - + +
46O VAL* 3.8 26.0 - - + -
62O LYS* 3.2 48.5 - - + -
63O LEU 3.9 5.6 - - - -
64O PHE* 3.7 29.2 - + + -
125O ASP* 3.3 24.2 - - + +
126O GLY 5.6 0.2 - - - +
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Residues in contact with LYS 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C PRO 4.7 11.7 + - - -
264C THR* 5.8 1.2 - - - +
265C LEU 5.9 0.2 + - - -
267C ASP* 4.9 6.7 - - - -
280C THR* 4.7 19.5 - - + -
281C SER* 5.2 11.1 - - - -
21O TYR* 3.9 26.7 + - + -
22O GLY 3.2 8.1 - - - -
23O GLU* 4.6 8.3 - - - +
33O PHE* 1.4 72.1 - - - +
35O VAL* 1.3 59.3 + - - +
123O GLU 3.5 13.2 + - - +
124O PHE* 3.0 29.0 - - + +
125O ASP* 2.5 33.4 + - - +
126O GLY 3.2 4.0 + - - -
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Residues in contact with VAL 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O TYR* 2.8 7.3 - - - +
22O GLY 2.5 51.8 + - - +
24O ILE* 3.4 38.8 - - + -
33O PHE* 4.0 7.0 - - + +
34O LYS 1.3 72.7 - - - +
36O VAL* 1.3 69.2 + - - +
37O PHE* 3.9 15.3 - - + -
45O TRP 6.1 0.2 - - - +
46O VAL* 5.6 3.1 - - + -
124O PHE* 4.2 0.9 - - - -
126O GLY* 3.5 17.0 - - - +
128O VAL* 3.0 31.4 - - + -
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Residues in contact with VAL 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR 3.3 23.3 - - - +
21O TYR* 3.9 11.4 - - + +
35O VAL* 1.3 74.6 - - - +
37O PHE* 1.3 61.8 + - - +
38O ASP 3.7 0.7 + - - -
124O PHE* 3.9 18.2 - - + -
126O GLY 3.2 15.8 + - - +
127O VAL* 3.6 2.5 - - + +
128O VAL 3.0 23.2 + - - -
228O GLY* 5.3 1.3 - - - -
1341O C61 3.6 60.6 - - + +
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Residues in contact with PHE 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O VAL* 4.1 33.7 - - + -
12O LEU* 4.1 16.2 - - + -
20O TYR 4.7 2.8 + - - -
22O GLY* 4.2 5.4 - - - -
23O GLU 4.9 1.3 - - - -
24O ILE* 4.1 17.0 - - + -
35O VAL* 3.9 20.6 - - + -
36O VAL* 1.3 74.8 - - - +
38O ASP* 1.4 53.8 + - - +
99O VAL* 5.3 9.2 - - + -
128O VAL* 3.6 33.4 - - + -
130O MET* 4.2 18.8 - - + -
160O PHE* 3.8 8.9 - - + -
162O TYR* 4.3 0.9 + - - -
176O ILE* 3.7 31.9 - - + -
178O LEU* 5.8 5.4 - - + -
227O THR* 2.7 34.1 + - - +
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Residues in contact with ASP 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O VAL 3.7 0.8 + - - -
37O PHE* 1.4 69.2 - - - +
39O THR* 1.3 60.5 + - - +
40O GLY 3.3 0.9 - - - -
41O SER* 2.4 36.1 + - - +
127O VAL* 4.0 13.7 - - + -
128O VAL 3.2 7.3 + - - +
129O GLY* 4.4 0.4 - - - -
130O MET* 2.3 37.8 + - - +
226O ASP* 4.0 1.1 - - - -
227O THR* 3.8 1.6 - - - -
228O GLY* 3.0 27.6 - - - +
1341O C61 2.6 45.3 + - - +
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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
------------------------------------------------------------
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