Contacts of the strand formed by residues 25 - 30 (chain B) in PDB entry 2E3V
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.2 9.6 - - + -
19B GLU 3.4 9.4 - - - +
20B PRO* 4.1 5.2 - - + -
21B TYR* 4.6 0.2 - - - -
24B THR* 1.3 76.6 - - - +
26B GLN* 1.3 63.5 + - - +
27B VAL* 3.7 1.9 + - + -
71B VAL 3.8 0.2 - - - +
72B THR* 3.4 3.4 - - - -
73B ILE* 2.8 40.4 + - + +
76B LEU* 4.0 2.9 - - + -
103B PHE* 3.7 35.9 - - + -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN 3.7 1.7 - - - +
18B VAL* 3.2 3.8 - - - -
19B GLU* 2.8 49.7 + - + +
21B TYR* 3.2 35.7 + - + -
24B THR* 5.8 0.2 - - - +
25B ALA* 1.3 71.7 - - - +
27B VAL* 1.3 61.6 + - - +
28B GLN* 3.9 0.4 - - - -
70B ILE* 3.7 24.5 - - + +
71B VAL 3.7 4.3 - - - -
72B THR* 3.7 21.6 + - + +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.9 40.2 - - + -
17B GLN 3.6 2.7 - - - -
18B VAL* 4.2 17.5 - - + +
25B ALA* 4.3 3.1 - - + +
26B GLN* 1.3 74.4 - - - +
28B GLN* 1.3 62.7 + - - +
29B PHE* 3.9 3.1 - - - -
69B GLY 3.8 0.5 - - - +
70B ILE* 3.4 4.7 - - - +
71B VAL* 2.8 43.1 + - + +
73B ILE* 3.9 26.7 - - + -
84B VAL* 4.3 13.2 - - + -
86B LEU* 4.1 16.8 - - + -
103B PHE* 5.2 0.7 - - + -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.7 4.2 - - - +
16B ASP* 2.8 24.6 + - - -
17B GLN* 2.7 47.6 + - + +
19B GLU* 5.9 1.6 - - - +
26B GLN* 3.9 1.0 + - + -
27B VAL* 1.3 72.5 - - - +
29B PHE* 1.3 60.8 + - - +
68B GLU* 3.1 20.3 - - - +
69B GLY 3.2 3.1 - - - +
70B ILE* 4.1 19.0 - - + +
44C LYS* 4.7 0.8 - - - +
57C SER* 2.9 43.7 + - - +
58C LYS* 3.9 1.6 - - - -
59C TRP* 3.5 20.4 - - + +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.8 14.6 - - + -
14B SER 3.0 17.9 - - - +
15B ILE* 4.2 0.7 - - - -
16B ASP* 3.6 5.4 - - - -
27B VAL 3.9 7.4 - - - -
28B GLN* 1.3 75.1 - - - +
30B ASP* 1.3 69.5 + - - +
31B GLU* 4.2 3.4 - - + -
43B TYR* 3.4 53.6 - + - -
65B ALA* 4.2 4.3 - - + -
66B SER* 6.1 0.2 - - - -
69B GLY* 2.8 49.2 + - - +
70B ILE 3.7 4.3 - - - -
71B VAL* 3.9 20.9 - - + -
86B LEU* 3.6 30.5 - - + -
58C LYS* 5.2 0.9 - - - +
59C TRP* 4.0 12.0 + - - +
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.4 6.1 - - - +
14B SER* 2.9 38.6 + - - -
16B ASP* 2.5 26.7 + - - +
29B PHE* 1.3 75.8 - - - +
31B GLU* 1.3 64.3 + - - +
32B PRO* 4.9 2.1 - - - +
42C LYS* 2.8 28.0 + - - +
58C LYS* 6.2 1.3 - - - +
59C TRP 3.4 20.4 - - - +
60C TYR* 4.0 0.7 - - - -
61C ASP* 3.3 35.4 - - - +
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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