Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 5EEV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.6 1.1 - - + -
14B ALA* 3.8 10.3 - - + -
16B GLU* 3.5 22.4 - - + +
17B ASP 3.4 0.8 + - - -
18B GLY* 1.3 76.0 - - - +
20B ASN* 1.3 61.6 + - - +
21B VAL* 4.6 0.7 - - + -
36B GLU 3.8 0.9 - - - +
37B LYS* 3.1 5.2 - - - -
38B LEU* 2.7 54.0 + - + +
57B VAL* 4.1 19.1 - - + -
58B ARG 3.4 12.8 - - - +
59B GLY* 4.2 1.8 - - - -
60B LYS 3.2 34.1 - - - +
61B ALA* 4.1 8.3 - - + -
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Residues in contact with ASN 20 (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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18B GLY 3.2 5.8 + - - +
19B VAL* 1.3 72.8 - - - +
21B VAL* 1.3 61.3 + - - +
22B ILE* 3.8 16.8 + - + +
35B SER* 2.6 39.5 + - - -
36B GLU 3.8 4.9 + - - +
37B LYS* 4.4 16.0 - - + +
56B LYS 3.5 4.7 - - - +
57B VAL* 3.6 1.2 - - - -
58B ARG* 3.0 49.3 + - + +
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Residues in contact with VAL 21 (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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101A TRP* 4.3 14.1 - - + -
12B ILE* 3.6 35.4 - - + -
19B VAL* 4.6 2.7 - - + -
20B ASN* 1.3 73.3 - - - +
22B ILE* 1.4 60.6 + - - +
23B GLY 4.2 0.3 + - - -
34B HIS 3.9 1.0 - - - +
35B SER* 3.4 1.6 - - - -
36B GLU* 2.7 46.3 + - - +
38B LEU* 3.9 21.3 - - + -
44B LEU* 3.8 28.0 - - + -
46B ALA* 5.3 1.1 - - + -
55B ILE* 3.9 17.3 - - + -
56B LYS 3.6 3.6 - - - +
57B VAL* 4.8 2.9 - - + +
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Residues in contact with ILE 22 (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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101A TRP* 4.0 2.5 - - - -
20B ASN* 3.8 24.0 - - - +
21B VAL* 1.4 75.6 - - - +
23B GLY* 1.4 56.5 + - - +
24B LEU* 3.8 11.3 - - + +
32B PHE* 3.6 34.1 - - + -
34B HIS 3.5 5.6 - - - +
35B SER* 4.4 3.8 - - - -
55B ILE* 3.3 5.0 - - - -
56B LYS* 2.7 60.7 + - + +
58B ARG* 3.8 37.9 - - + +
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Residues in contact with GLY 23 (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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101A TRP* 3.4 28.7 - - - -
22B ILE* 1.4 69.8 - - - +
24B LEU* 1.4 61.6 + - - -
32B PHE* 3.3 4.7 - - - -
33B HIS* 2.9 34.8 + - - -
34B HIS 2.9 11.6 + - - -
52B THR* 3.9 6.1 - - - -
54B ALA 3.8 4.5 - - - -
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Residues in contact with LEU 24 (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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22B ILE* 3.8 26.2 - - + +
23B GLY* 1.4 78.5 - - - +
25B THR* 1.4 67.2 + - - +
30B THR* 3.9 20.4 - - + -
31B ARG* 3.5 11.2 - - - +
32B PHE* 4.6 3.4 - - + -
33B HIS* 4.0 1.8 - - - -
52B THR* 3.3 5.5 - - - -
53B SER* 3.2 20.8 + - - -
54B ALA* 2.8 37.5 + - + +
56B LYS* 4.5 10.3 - - + -
101B TRP* 5.1 1.8 - - + -
34C HIS* 5.1 0.4 - - + +
36C GLU* 3.9 34.8 - - + +
44C LEU* 4.2 10.3 - - + -
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Residues in contact with THR 25 (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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24B LEU* 1.4 73.5 - - - +
26B ARG* 1.3 64.8 + - - +
29B ASP* 2.8 27.1 + - - +
30B THR* 4.5 0.5 - - - -
31B ARG* 2.9 43.3 + - + +
33B HIS* 3.7 25.3 - - + -
51B HIS 3.4 7.4 - - - +
53B SER* 3.7 2.0 + - - -
101B TRP* 2.8 25.3 + - - +
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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
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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