Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 5V5W
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.4 26.2 + - + +
30A VAL* 3.7 13.2 - - - +
31A HIS* 2.9 53.4 + - - +
38A VAL* 4.0 7.7 - - + +
39A LYS 4.4 1.8 - - - +
40A GLU* 3.8 26.7 - - + +
44A SER* 1.3 84.1 + - - +
46A ARG* 1.3 61.5 + - - +
121A SER 3.9 14.6 - - - +
122A ILE* 3.9 21.1 - - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 2.7 17.9 + - + +
40A GLU* 4.6 3.6 - - - -
41A ASP* 3.0 30.7 + - + +
43A ILE* 3.7 24.0 - - - +
44A SER* 2.6 33.8 + - - +
45A GLU* 1.3 78.8 + - - +
47A VAL* 1.3 64.5 + - + +
105A ARG* 5.0 3.9 + - - +
121A SER 4.6 8.0 + - - -
122A ILE* 3.4 6.9 - - - +
123A ARG* 3.0 25.5 + - - +
301A SO4 3.7 24.5 + - - +
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Residues in contact with VAL 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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38A VAL* 3.3 13.2 - - - +
39A LYS* 3.0 53.7 + - + +
46A ARG* 1.3 86.4 - - + +
48A TYR* 1.3 63.9 + - - +
49A THR* 3.6 20.2 - - - +
122A ILE* 3.9 3.6 - - - +
123A ARG* 3.2 47.1 - - - +
125A ASP* 4.4 6.3 - - + -
301A SO4 3.8 17.0 - - - +
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Residues in contact with TYR 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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31A HIS* 3.7 19.3 - - + -
32A ALA 2.7 29.1 + - - -
34A GLN 3.6 10.4 + - - -
35A ALA* 3.5 21.4 + - + -
37A VAL 4.0 2.0 - - - -
38A VAL* 4.6 1.6 - - + -
47A VAL* 1.3 71.6 - - - +
49A THR* 1.3 62.0 + - - +
50A ILE* 4.0 15.0 - - + -
56A LEU* 3.5 39.8 - - + -
57A MET 3.1 28.2 + - - -
58A LEU* 3.4 15.9 - - + -
122A ILE* 4.0 13.7 - - + +
123A ARG 2.7 10.9 + - - +
124A VAL* 3.3 11.3 - - + +
125A ASP 2.9 23.4 + - - +
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Residues in contact with THR 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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35A ALA* 3.1 7.2 - - - +
36A CYS 2.7 29.7 + - - -
37A VAL* 2.9 34.0 + - + +
39A LYS* 5.1 4.0 - - - -
47A VAL* 3.6 19.2 - - - +
48A TYR* 1.3 70.7 - - - +
50A ILE* 1.3 57.6 + - - +
125A ASP* 3.4 17.0 + - - +
127A GLN* 3.5 38.4 - - + +
222A CYS* 4.1 5.6 - - - -
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Residues in contact with ILE 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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34A GLN 3.6 20.4 - - - +
35A ALA* 4.0 0.7 - - - -
36A CYS* 3.8 8.5 - - - -
48A TYR* 4.0 20.4 - - + -
49A THR* 1.3 77.7 - - - +
51A ARG* 1.3 66.0 + - - +
54A ASP* 3.7 11.4 - - + -
55A THR 3.5 44.0 - - - +
56A LEU* 3.6 8.7 - - + +
98A ILE* 4.1 26.2 - - + -
124A VAL* 4.4 5.4 - - + -
125A ASP 3.0 7.6 + - - +
126A VAL* 3.3 5.4 - - + -
127A GLN 3.0 21.6 + - - -
222A CYS* 4.2 1.6 - - - -
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Residues in contact with ARG 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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36A CYS* 3.8 5.7 - - - -
50A ILE* 1.3 78.3 - - - +
52A GLU* 1.3 81.3 + - + +
53A GLY 3.1 0.2 + - - -
54A ASP* 2.9 40.2 + - - +
98A ILE* 3.9 2.0 - - - +
126A VAL* 4.4 0.7 - - - -
127A GLN 3.6 7.4 - - - +
128A TYR* 5.8 0.2 - - - -
222A CYS* 3.9 22.8 + - + +
223A GLY 2.9 27.8 + - - -
224A ILE* 3.7 26.6 - - + +
225A PRO* 3.8 18.2 - - - +
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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