Contacts of the strand formed by residues 38 - 47 (chain A) 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 GLU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A MET* 3.1 3.7 - - - +
35A ILE* 2.9 36.8 + - - +
36A ASP 2.7 11.6 + - - +
37A SER* 1.3 71.9 - - - +
39A PRO* 1.3 74.2 - - + +
40A LEU* 3.5 10.6 + - - +
163A ARG* 3.6 31.7 + - - -
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Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL 3.9 3.4 - - - +
34A MET* 3.7 12.1 - - + -
37A SER 3.4 9.4 - - - +
38A GLU* 1.3 94.1 - - + +
40A LEU* 1.3 64.1 + - - +
41A GLY* 4.9 2.7 - - - +
163A ARG* 5.3 1.4 + - - -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 2.9 23.2 + - + +
35A ILE* 3.2 41.5 - - + +
38A GLU* 3.5 15.5 + - - +
39A PRO* 1.3 74.7 - - - +
41A GLY* 1.3 60.3 + - - +
160A VAL* 4.1 21.4 - - + +
163A ARG* 3.1 48.9 + - + +
164A ILE* 3.7 25.6 - - + -
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.5 3.6 - - - +
33A VAL* 2.8 29.9 + - - +
39A PRO* 3.6 3.0 - - - +
40A LEU* 1.3 81.7 - - - +
42A ARG* 1.3 61.8 + - - -
160A VAL* 4.3 9.2 - - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.5 40.1 + - + -
31A PHE 3.3 6.1 - - - +
32A ASP* 2.7 43.2 + - - +
41A GLY* 1.3 73.3 - - - -
43A ILE* 1.3 74.8 + - - +
44A THR* 3.8 12.9 + - - +
156A ASP* 3.9 3.1 - - - +
157A GLY* 3.4 18.9 - - - -
160A VAL* 4.0 6.0 - - - +
187A LEU* 4.4 14.4 - - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.2 4.3 - - - -
31A PHE* 2.8 50.4 + - + +
33A VAL* 3.8 22.4 - - + -
42A ARG* 1.3 75.9 - - - +
44A THR* 1.3 60.7 + - - +
45A ILE* 3.7 19.6 + - + +
76A PHE* 4.8 7.0 - - + -
85A ILE* 5.2 0.2 - - + -
136A ILE* 4.8 5.2 - - + -
154A VAL* 4.1 20.0 - - + -
156A ASP 3.7 2.5 - - - -
157A GLY* 4.1 6.7 - - - +
160A VAL* 3.9 19.3 - - + -
161A VAL* 3.8 30.3 - - + -
164A ILE* 4.4 9.0 - - + -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 4.8 6.5 - - + -
29A VAL 3.6 10.3 - - - +
30A TYR* 4.4 1.5 - - - +
42A ARG* 3.8 19.2 + - - +
43A ILE* 1.3 71.5 - - - +
45A ILE* 1.3 65.9 + - - +
154A VAL* 3.6 3.5 - - - +
155A LEU* 2.8 41.7 + - + -
156A ASP* 2.7 35.9 + - + +
187A LEU* 4.1 22.6 - - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.2 8.1 - - - +
29A VAL* 2.8 57.8 + - + +
31A PHE* 3.9 34.3 - - + -
43A ILE* 4.1 20.4 - - + +
44A THR* 1.3 78.3 - - - +
46A GLY* 1.3 74.5 + - - +
47A LEU* 4.1 7.0 - - + -
59A PHE* 4.5 4.5 - - + -
120A LEU* 3.9 37.7 - - + -
136A ILE* 4.7 3.1 - - + -
153A LYS 3.5 8.7 - - - +
154A VAL* 4.6 2.2 - - + -
155A LEU* 4.2 3.3 - - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.7 12.3 - - - -
27A ALA 3.6 7.4 - - - -
45A ILE* 1.3 78.0 - - - +
47A LEU* 1.3 60.9 + - - -
48A PHE* 5.1 0.2 - - - -
152A GLY* 3.1 6.1 - - - -
153A LYS 2.8 34.7 + - - -
155A LEU* 3.6 22.1 - - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.7 2.2 - - - +
26A THR* 2.9 24.9 + - - +
27A ALA* 3.0 30.5 + - + +
29A VAL* 3.9 31.2 - - + -
45A ILE* 4.1 10.5 - - + -
46A GLY* 1.3 79.5 - - - +
48A PHE* 1.3 56.1 + - - +
49A GLY 2.7 15.5 + - - +
56A THR* 4.0 31.4 - - + +
59A PHE* 3.9 22.9 - - + -
60A ARG* 4.3 7.6 - - + -
151A PHE* 3.8 24.0 - - + +
152A GLY* 4.7 0.7 - - - -
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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