Contacts of the strand formed by residues 102 - 107 (chain B) in PDB entry 4LAV
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.8 2.8 - - - +
38B LYS* 2.8 47.9 + - + -
39B ARG* 2.9 64.3 + - + +
101B GLU* 1.3 72.6 - - - +
103B CYS* 1.3 65.0 + - - +
131B GLU* 3.9 21.1 - - + +
132B VAL 3.3 11.4 - - - +
133B GLU* 3.6 22.4 - - + +
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Residues in contact with CYS 103 (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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35B LYS* 3.6 25.6 - - + -
36B VAL 3.4 13.7 - - - +
37B ILE* 4.4 0.9 - - - -
38B LYS 4.1 0.7 - - - +
93B ALA* 4.8 4.5 - - - -
97B MET* 3.8 25.9 - - + +
101B GLU* 3.8 5.6 - - - +
102B VAL* 1.3 75.2 - - - +
104B HIS* 1.3 72.2 + - - +
105B ILE* 3.9 22.7 - - - -
131B GLU* 4.0 0.7 - - - +
132B VAL* 2.8 42.0 + - - -
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Residues in contact with HIS 104 (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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16A ALA* 4.8 2.7 - - - -
17A PRO* 3.3 44.2 - - + +
18A LEU 4.7 2.5 + - - +
20A MET* 3.7 6.0 - - + +
18B LEU* 3.8 22.5 - - + +
35B LYS* 3.4 2.4 - - - -
36B VAL* 2.8 45.5 + - + +
38B LYS* 3.4 22.6 - - + +
103B CYS* 1.3 84.6 - - - +
105B ILE* 1.3 63.9 + - - +
130B PHE 3.2 3.6 - - - -
131B GLU* 2.9 35.9 + - + -
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Residues in contact with ILE 105 (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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20A MET* 4.5 0.7 - - - -
33B VAL* 4.7 8.5 - - + -
34B LEU 3.0 11.4 - - - +
35B LYS* 3.8 17.0 - - + -
89B ALA* 4.1 13.0 - - + +
90B TRP* 4.1 14.6 - - + -
93B ALA* 3.9 26.7 - - + -
103B CYS* 3.9 15.7 - - - -
104B HIS* 1.3 81.0 - - - +
106B THR* 1.3 63.8 + - - +
107B CYS* 4.1 1.1 - - + -
128B LEU 3.8 0.3 - - - +
129B VAL* 3.2 9.1 - - - +
130B PHE* 2.8 67.7 + - + +
132B VAL* 4.5 7.9 - - + -
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Residues in contact with THR 106 (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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18A LEU 4.0 1.7 + - - -
19A PRO* 3.6 9.4 - - + +
20A MET* 2.9 55.9 + - - +
21A GLU* 5.9 0.4 - - - +
31B GLU 5.3 0.2 - - - +
32B GLY 3.9 0.7 - - - +
33B VAL* 3.5 2.1 - - - -
34B LEU* 2.9 36.4 + - + +
105B ILE* 1.3 76.8 + - - +
107B CYS* 1.3 61.9 + - - +
108B LYS* 5.8 1.1 - - + +
127B THR* 3.7 25.1 - - + -
128B LEU 3.3 6.5 - - - +
129B VAL* 3.8 9.2 - - + +
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Residues in contact with CYS 107 (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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32B GLY 3.3 7.6 - - - +
33B VAL* 4.6 2.7 - - + -
89B ALA* 3.5 31.4 - - + -
105B ILE* 5.3 2.2 - - + -
106B THR* 1.3 75.5 - - - +
108B LYS* 1.3 67.3 + - - +
111B TYR* 4.4 1.3 - - + -
112B ALA* 4.0 13.5 - - - -
126B ALA 4.2 0.5 - - - +
127B THR* 3.4 7.0 - - - +
128B LEU* 2.8 45.3 + - - +
130B PHE* 3.7 32.5 - - - -
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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