Contacts of the strand formed by residues 35 - 42 (chain A) in PDB entry 1EVW
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 LEU 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO* 3.6 5.4 - - - +
31A LEU* 2.9 37.1 + - + -
32A GLY 2.8 12.9 + - - +
33A GLY* 3.0 16.1 - - - +
34A GLY* 1.3 81.6 - - - +
36A GLN* 1.3 66.0 + - - +
129A ASN* 3.9 28.3 - - - +
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Residues in contact with GLN 36 (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 HIS* 3.4 49.3 + - - +
29A VAL 3.6 13.8 - - - +
30A PRO* 4.5 5.5 - - + +
31A LEU* 3.0 9.6 - - - +
34A GLY 4.2 1.1 + - - +
35A LEU* 1.3 81.1 - - - +
37A GLY* 1.3 57.4 - - - +
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Residues in contact with GLY 37 (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 HIS* 3.3 14.1 - - - +
29A VAL* 2.9 34.0 + - - -
31A LEU* 3.1 19.1 - - - +
36A GLN* 1.3 74.3 - - - +
38A THR* 1.3 64.4 + - - -
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Residues in contact with THR 38 (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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26A THR* 3.7 27.8 - - + -
27A HIS 3.3 12.6 - - - +
28A HIS* 3.8 17.8 + - + +
29A VAL* 5.3 0.2 - - - -
31A LEU* 5.1 0.2 - - - +
37A GLY* 1.3 77.2 + - - -
39A LEU* 1.3 78.7 + - - +
40A HIS* 4.5 9.8 - - - +
163B VAL* 4.1 8.3 - - - +
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Residues in contact with LEU 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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25A ILE 3.4 0.4 - - - +
26A THR* 3.3 5.0 - - - +
27A HIS* 2.7 43.8 + - + +
29A VAL* 4.1 26.0 - - + -
31A LEU* 5.8 2.7 - - + -
38A THR* 1.3 94.7 - - - +
40A HIS* 1.3 65.0 + - - +
41A CYS* 4.1 3.4 - - - +
100A CYS* 4.2 24.0 - - + -
110A HIS* 3.6 18.6 - - + +
139A LEU* 4.1 33.2 - - + +
140A ARG* 4.7 1.3 - - + -
163B VAL* 3.5 21.1 - - + -
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Residues in contact with HIS 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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24A VAL* 3.8 22.2 - - + -
25A ILE 3.1 5.6 - - - -
26A THR* 3.3 35.8 - - + +
38A THR* 4.5 10.3 - - + +
39A LEU* 1.3 77.0 - - - +
41A CYS* 1.3 63.3 + - - +
42A TYR* 3.6 4.4 - - + -
107A ASN* 3.4 13.9 + - - -
110A HIS* 3.3 15.0 - - - -
162B VAL* 4.0 22.4 - - + +
163B VAL* 2.6 43.4 + - - +
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Residues in contact with CYS 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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24A VAL* 3.5 2.3 - - - -
25A ILE* 2.8 39.6 + - - +
27A HIS* 4.5 10.3 - - + -
39A LEU* 4.1 3.6 - - - -
40A HIS* 1.3 75.3 - - - +
42A TYR* 1.3 61.7 + - - +
43A GLU* 3.4 10.6 + - + +
100A CYS* 3.4 13.7 - - - -
102A ASN* 3.6 21.1 - - - +
105A CYS* 3.3 18.4 - - + -
110A HIS* 3.7 4.0 - - - -
502A ZN 2.2 33.9 - - - -
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Residues in contact with TYR 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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19A VAL* 4.0 7.0 - - + +
20A GLY 3.8 16.8 - - - -
22A PHE* 3.8 20.5 - - + -
23A PRO 3.5 8.5 - - - -
24A VAL* 3.5 29.9 - - + +
40A HIS* 3.6 13.5 - - + -
41A CYS* 1.3 70.7 - - - +
43A GLU* 1.3 62.0 + - - +
44A ILE 3.7 0.9 + - - -
104A ARG 3.6 0.7 - - - +
105A CYS* 3.7 6.0 - - - -
106A HIS 3.0 19.6 + - - -
107A ASN* 3.3 38.8 - - + +
160B HIS 3.4 9.3 + - - -
161B PHE* 3.0 54.2 - + + -
162B VAL* 3.3 16.3 + - - +
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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