Contacts of the strand formed by residues 39 - 47 (chain B) in PDB entry 3EOV
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 PRO 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B VAL 3.9 5.8 - - - +
34B MET* 3.4 22.4 - - + -
37B SER 3.7 3.4 - - - +
38B GLU* 1.3 95.5 - - + +
40B LEU* 1.3 63.0 + - - +
41B GLY* 4.9 2.7 - - - +
163B ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 40 (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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33B VAL* 3.0 16.0 + - + +
34B MET 4.0 1.3 - - - -
35B ILE* 3.2 48.0 - - + +
38B GLU* 3.2 28.0 - - - +
39B PRO* 1.3 76.2 - - - +
41B GLY* 1.3 59.4 + - - +
160B VAL* 3.8 22.6 - - + +
163B ARG* 3.7 36.9 + - + +
164B ILE* 3.7 26.0 - - + -
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Residues in contact with GLY 41 (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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31B PHE 3.7 0.3 - - - +
32B ASP* 3.5 4.8 - - - -
33B VAL* 2.7 37.3 + - - +
39B PRO* 3.6 3.5 - - - +
40B LEU* 1.3 82.8 - - - +
42B ARG* 1.3 57.7 + - - -
160B VAL* 4.1 8.3 - - - -
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Residues in contact with ARG 42 (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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30B TYR* 3.5 38.9 + - + -
31B PHE 3.2 6.7 - - - +
32B ASP* 2.9 39.1 + - - +
41B GLY* 1.3 73.0 - - - -
43B ILE* 1.3 68.9 + - - +
44B THR* 4.0 19.5 + - - +
156B ASP* 4.2 1.2 - - - +
157B GLY* 3.5 19.1 - - - -
160B VAL* 3.8 4.8 - - - +
187B LEU* 4.2 20.7 - - - +
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Residues in contact with ILE 43 (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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30B TYR* 3.1 5.7 - - - -
31B PHE* 2.8 47.7 + - + +
33B VAL* 4.0 16.6 - - + -
42B ARG* 1.3 72.5 - - - +
44B THR* 1.3 61.4 + - - +
45B ILE* 3.7 20.1 + - + +
76B PHE* 4.9 5.6 - - + -
85B ILE* 5.3 0.4 - - + -
136B ILE* 4.5 7.2 - - + -
154B VAL* 4.0 25.6 - - + -
156B ASP 3.6 3.6 - - - +
157B GLY 4.1 1.3 - - - +
160B VAL* 3.7 31.2 - - + -
161B VAL* 3.9 23.1 - - + -
164B ILE* 4.6 8.1 - - + -
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Residues in contact with THR 44 (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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28B LYS* 4.8 7.6 - - + +
29B VAL 3.7 8.7 - - - +
30B TYR* 4.4 0.8 - - - +
42B ARG* 4.0 19.3 - - - +
43B ILE* 1.3 71.5 - - - +
45B ILE* 1.3 58.1 + - - +
154B VAL* 3.6 2.8 - - - -
155B LEU* 2.7 54.1 + - + -
156B ASP* 2.8 31.2 + - + +
187B LEU* 4.4 19.5 - - + +
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Residues in contact with ILE 45 (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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28B LYS* 3.3 6.8 - - - +
29B VAL* 2.9 52.2 + - + +
30B TYR* 5.9 0.4 - - - -
31B PHE* 3.9 32.1 - - + -
43B ILE* 4.1 13.7 - - + +
44B THR* 1.3 77.7 - - - +
46B GLY* 1.3 75.0 + - - +
47B LEU* 4.3 7.9 - - + -
59B PHE* 4.3 7.4 - - + -
120B LEU* 3.4 42.8 - - + -
136B ILE* 4.3 8.3 - - + -
153B LYS 3.6 4.5 - - - +
154B VAL* 4.5 4.0 - - + -
155B LEU* 4.1 3.1 - - - -
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Residues in contact with GLY 46 (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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25B VAL* 3.9 13.5 - - - -
27B ALA 3.6 6.5 - - - -
45B ILE* 1.3 76.7 - - - +
47B LEU* 1.3 61.9 + - - -
48B PHE* 4.3 0.7 - - - -
152B GLY* 3.1 5.4 - - - -
153B LYS 2.8 34.7 + - - -
155B LEU* 3.6 21.7 - - - +
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Residues in contact with LEU 47 (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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25B VAL* 3.1 4.7 - - - +
26B THR* 2.8 32.6 + - - +
27B ALA* 2.9 34.9 + - + +
29B VAL* 4.1 29.4 - - + -
45B ILE* 4.3 8.3 - - + -
46B GLY* 1.3 77.7 - - - +
48B PHE* 1.3 60.4 + - - +
49B GLY 3.2 1.2 + - - +
56B THR* 4.0 29.4 - - + +
59B PHE* 3.9 18.8 - - + -
60B ARG* 4.5 6.3 - - + -
151B PHE* 3.6 32.1 - - + +
152B GLY* 4.8 0.2 - - - -
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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