Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 1EWV
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 3.7 0.3 - - - -
44A ASP* 1.3 80.7 - - + +
46A ILE* 1.3 69.0 + - - +
47A ILE* 4.4 0.7 - - + -
99A ILE* 3.6 30.1 - - + -
100A THR 2.8 4.5 + - - +
101A LEU* 3.3 15.9 - - + -
102A GLY* 2.4 34.8 + - - -
157A ALA* 4.1 17.7 - - + -
424A LEU* 3.4 35.4 - - + -
438A LEU* 4.7 12.8 - - + -
445A ILE* 4.3 10.5 - - + -
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Residues in contact with ILE 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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41A MET 4.3 4.5 - - - +
42A ASP* 4.7 3.4 - - - +
43A GLY 3.7 17.3 - - - +
44A ASP 5.2 0.2 - - - +
45A VAL* 1.3 89.6 - - - +
47A ILE* 1.3 59.2 + - - +
102A GLY* 3.2 19.7 - - - +
103A SER* 4.1 13.7 - - - +
104A GLU* 4.6 11.4 - - + +
154A LYS* 4.1 34.8 - - + +
155A PRO 4.5 6.4 + - - +
156A ILE* 3.4 25.5 - - + +
157A ALA* 2.5 35.6 + - - +
445A ILE* 5.8 0.4 - - - +
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Residues in contact with ILE 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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45A VAL* 4.4 0.4 - - + -
46A ILE* 1.3 75.9 - - - +
48A GLY* 1.3 65.4 + - - +
82A MET* 3.9 6.5 - - + +
86A LEU* 5.7 5.8 - - + -
101A LEU* 3.4 38.6 - - + -
102A GLY 2.6 12.6 + - - +
103A SER* 2.8 32.6 - - - -
104A GLU 4.2 0.4 - - - -
156A ILE* 4.3 0.2 - - - -
157A ALA* 4.4 10.8 - - + -
158A GLY 3.2 17.3 - - - +
160A ILE* 4.2 11.7 - - + -
417A ILE 5.1 2.5 - - - +
420A MET* 3.2 39.7 - - + +
421A ALA 4.8 0.4 - - - +
424A LEU* 4.4 6.3 - - + -
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Residues in contact with GLY 48 (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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47A ILE* 1.3 76.2 - - - +
49A ALA* 1.3 61.6 + - - +
104A GLU* 3.5 13.9 - - - -
122A PHE* 4.4 6.7 - - - -
156A ILE* 3.4 22.5 - - - +
158A GLY 2.8 15.6 + - - +
159A VAL* 3.0 7.2 - - - -
160A ILE 2.8 20.0 + - - -
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Residues in contact with ALA 49 (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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47A ILE 4.1 0.4 + - - -
48A GLY* 1.3 74.4 - - - +
50A LEU* 1.3 69.6 + - - +
51A PHE* 4.0 17.3 - - + -
82A MET* 3.3 27.1 - - + -
104A GLU 3.2 7.9 + - - +
105A ILE* 4.6 4.3 - - + -
106A ARG 3.0 25.1 + - - -
122A PHE* 4.3 1.4 - - - -
159A VAL* 4.5 1.6 - - - -
160A ILE* 3.1 22.0 - - + +
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Residues in contact with LEU 50 (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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49A ALA* 1.3 87.2 - - - +
51A PHE* 1.3 61.0 + - - +
106A ARG* 3.4 18.4 - - + +
107A ASP 5.6 0.7 - - - +
108A SER* 4.3 7.6 - - - -
115A ALA* 4.5 11.4 - - + +
118A GLN* 4.5 7.2 - - + -
119A SER* 3.6 22.2 - - - +
122A PHE* 3.6 24.5 - - + -
159A VAL* 4.3 11.2 - - + -
160A ILE 2.7 9.8 + - - +
161A GLY* 3.9 1.9 - - - -
162A PRO* 3.5 39.6 - - + +
163A GLY 3.9 1.0 + - - -
171A VAL* 3.9 23.1 - - + -
185A TYR* 3.7 9.9 + - - -
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Residues in contact with PHE 51 (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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49A ALA* 4.0 20.9 - - + -
50A LEU* 1.3 75.3 - - - +
52A SER* 1.3 60.5 + - - +
53A VAL* 3.1 7.2 + - + +
74A TYR 4.2 6.5 - - - +
78A ARG* 3.0 52.9 - - + -
79A VAL* 4.4 12.1 - - + -
82A MET* 3.5 24.0 - - + -
105A ILE* 3.9 19.3 - - + -
106A ARG 3.2 6.0 + - - +
107A ASP* 3.0 8.7 - - - +
108A SER* 3.0 20.6 + - - -
160A ILE* 4.8 4.7 - - + -
185A TYR* 3.6 25.4 - + - -
413A VAL* 3.5 28.0 - - + -
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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