Contacts of the strand formed by residues 25 - 32 (chain D) in PDB entry 2G94
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 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D THR* 3.1 3.0 - - - -
20D VAL* 2.9 46.1 + - + +
23D PRO* 3.9 6.8 + - + +
24D PRO* 1.3 75.7 - - - +
26D THR* 1.3 62.8 + - - +
27D LEU* 3.7 7.1 + - + +
51D TYR 3.8 5.4 - - - +
52D TYR* 3.5 14.5 - - - -
53D GLN* 2.8 55.3 + - - +
56D LEU* 4.1 15.5 + - - +
57D SER* 4.2 14.8 - - - -
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.6 38.0 + - + +
18D MET 3.4 5.6 - - - +
19D THR* 4.0 11.7 - - + +
24D PRO* 3.9 4.3 + - - +
25D GLN* 1.3 71.9 - - - +
27D LEU* 1.3 73.6 + - - +
50D ARG* 3.3 38.5 + - - +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 3.7 1.2 - - - +
18D MET* 2.8 36.1 + - + +
20D VAL* 3.6 32.3 - - + -
25D GLN* 3.7 7.6 + - + +
26D THR* 1.3 84.4 - - - +
28D ASN* 1.3 66.0 + - - +
29D ILE* 3.7 14.9 + - + +
40D VAL* 4.1 22.4 - - + -
41D GLY 5.6 0.2 - - - +
50D ARG* 3.9 21.1 - - + +
51D TYR* 4.1 23.1 - - - +
52D TYR* 4.2 13.0 - - + +
116D GLU* 3.5 13.5 - - + +
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Residues in contact with ASN 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ARG* 3.8 8.3 + - - +
15D TYR* 3.5 25.3 - - + -
16D VAL 3.7 1.8 - - - -
17D GLU* 3.9 22.0 + - - +
27D LEU* 1.3 75.0 + - - +
29D ILE* 1.3 60.4 + - - +
50D ARG* 3.3 21.0 + - - +
114D ASN* 2.9 47.5 + - - +
115D TRP* 3.4 3.1 - - - -
116D GLU* 2.7 39.7 + - - +
117D GLY 3.3 4.3 + - - -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR* 3.1 4.1 - - - +
16D VAL* 2.8 43.2 + - + +
18D MET* 3.6 28.0 - - + -
20D VAL* 6.1 0.4 - - + -
27D LEU* 3.8 22.2 - - + +
28D ASN* 1.3 81.6 - - - +
30D LEU* 1.3 63.5 + - - +
31D VAL 3.5 0.5 + - - -
38D PHE* 3.9 11.0 - - + -
40D VAL* 3.9 19.1 - - + -
117D GLY* 3.6 19.3 - - - +
118D ILE* 3.6 6.5 - - - -
119D LEU* 3.4 39.9 - - + +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY* 3.5 28.3 - - - -
14D TYR 3.5 18.4 - - - +
15D TYR* 3.8 4.1 - - - +
29D ILE* 1.3 71.3 - - - +
31D VAL* 1.3 65.8 + - - +
32D ASP* 3.4 9.6 + - + -
115D TRP* 3.7 27.8 - - + +
117D GLY 2.9 18.5 + - - +
118D ILE* 3.6 17.1 - - + +
119D LEU* 2.7 31.4 + - - +
229D SER 5.7 0.2 - - - +
230D GLY* 4.9 1.1 - - - -
4001D ZPQ 3.5 44.6 - - + -
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Residues in contact with VAL 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.1 22.2 - - + -
14D TYR* 2.9 22.9 + - + +
16D VAL* 4.2 9.9 - - + +
29D ILE 4.3 0.9 - - - +
30D LEU* 1.3 78.2 - - - +
32D ASP* 1.3 56.2 + - - +
119D LEU* 4.3 6.5 - - + -
121D LEU* 3.7 22.7 - - + -
152D LEU* 3.9 24.7 - - + -
154D LEU* 5.8 1.3 - - + -
174D MET* 4.0 22.9 - - + -
229D SER* 2.8 37.5 + - - +
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Residues in contact with ASP 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.4 5.8 + - + -
31D VAL* 1.3 74.6 - - - +
33D THR* 1.3 61.7 + - - +
34D GLY 3.3 2.8 + - - -
35D SER* 2.5 32.4 + - - +
118D ILE* 3.4 32.8 - - + +
119D LEU 3.1 10.4 + - - +
120D GLY* 3.3 4.0 - - - -
121D LEU* 2.9 23.6 + - - -
228D ASP* 3.0 11.4 - - - +
229D SER* 3.3 0.7 - - - -
230D GLY* 3.1 7.0 - - - -
4001D ZPQ 2.5 33.8 + - - +
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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