Contacts of the helix formed by residues 136 - 143 (chain B) in PDB entry 3RLP
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 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.6 14.4 - - + -
29B LEU* 4.0 14.8 - - + -
115B THR* 4.8 14.8 - - + +
118B PHE* 4.5 7.2 - - + -
131B ILE* 3.3 31.0 + - + +
134B PHE* 3.9 18.2 - - + +
135B GLY* 1.3 84.3 - - - +
137B GLY* 1.3 64.1 + - - +
138B PHE 3.1 4.7 + - - +
139B TYR* 3.1 38.8 + - + -
901B 3RP 5.2 1.8 - - - -
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Residues in contact with GLY 137 (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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47B GLU* 3.5 29.6 - - - +
48B LEU* 5.3 0.3 - - - +
51B ASN* 4.9 2.6 + - - +
131B ILE* 3.8 18.9 + - - -
132B GLY* 4.2 4.4 - - - -
135B GLY 3.6 2.4 + - - -
136B VAL* 1.3 76.8 - - - +
138B PHE* 1.3 59.2 + - - +
140B SER* 2.5 30.5 + - - -
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Residues in contact with PHE 138 (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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48B LEU* 3.9 21.1 - - + +
51B ASN* 3.8 15.7 - - - +
107B LEU* 4.3 7.4 - - + -
136B VAL* 3.1 0.8 - - - +
137B GLY* 1.3 76.5 - - - +
139B TYR* 1.3 80.9 + + - +
141B ALA* 3.0 28.1 + - + +
142B TYR* 4.6 4.9 - + - -
148B VAL* 3.9 21.1 - - + -
150B VAL* 3.8 30.7 - - + -
162B TRP* 3.9 23.8 - + - -
186B VAL* 4.3 9.2 - - + -
901B 3RP 3.5 52.5 - + + -
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Residues in contact with TYR 139 (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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22B PHE* 4.3 6.1 - + - -
26B ILE* 3.8 29.0 - - + +
29B LEU* 4.2 11.7 - - + -
30B MET* 3.9 32.3 - - + -
33B ILE* 3.5 25.7 - - + +
106B ASN 4.3 2.4 + - - -
107B LEU* 3.4 30.3 - - - -
108B GLY* 3.4 8.0 + - - -
136B VAL* 3.1 33.8 + - + +
137B GLY 3.1 1.2 + - - -
138B PHE* 1.3 96.3 - + - +
140B SER* 1.3 60.8 + - - +
141B ALA 2.9 6.9 + - - -
142B TYR* 3.1 24.1 + + - +
162B TRP* 5.1 1.8 - + - -
901B 3RP 4.0 15.0 - - + -
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Residues in contact with SER 140 (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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33B ILE* 4.2 6.5 - - - +
43B ILE* 4.0 13.7 - - - -
44B PHE* 3.4 25.7 + - - +
47B GLU* 3.5 7.3 - - - +
48B LEU* 5.7 0.3 - - - +
128B ILE* 5.1 1.1 - - - -
131B ILE* 4.2 12.2 - - - +
137B GLY 2.5 22.6 + - - -
139B TYR* 1.3 75.3 - - - +
141B ALA* 1.3 65.4 + - - +
142B TYR 3.0 0.4 - - - -
143B LEU* 2.9 42.6 + - - +
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Residues in contact with ALA 141 (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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44B PHE* 4.2 10.7 - - - +
48B LEU* 4.7 11.2 - - + +
138B PHE* 3.0 18.3 + - + +
139B TYR 2.9 0.4 - - - -
140B SER* 1.3 80.4 + - - +
142B TYR* 1.3 59.9 + - + +
143B LEU 3.1 0.2 - - - -
144B VAL* 3.1 9.9 + - - +
145B ALA* 2.9 26.8 + - - +
148B VAL* 3.9 14.1 - - + -
188B LEU* 3.8 26.5 - - + -
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Residues in contact with TYR 142 (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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30B MET* 3.6 26.2 - - + +
33B ILE* 3.8 7.6 - - + -
34B ILE* 3.8 25.7 - - + +
138B PHE* 4.6 9.2 - + - -
139B TYR* 3.1 30.4 + + + +
140B SER 3.0 1.6 - - - -
141B ALA* 1.3 74.9 - - + +
143B LEU* 1.3 61.2 + - - +
144B VAL 3.1 1.3 - - - -
145B ALA 3.6 17.3 - - - +
146B GLU 4.4 7.4 - - - -
148B VAL* 3.5 32.1 - - + +
162B TRP* 3.6 5.8 - + - -
164B SER* 2.9 40.2 + - - -
166B ALA* 4.0 22.4 - - + -
191B LYS* 3.0 24.8 + - - -
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Residues in contact with LEU 143 (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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33B ILE* 3.6 26.8 - - + +
36B THR 5.0 1.3 - - - +
38B TYR* 3.6 31.6 - - + -
41B LYS* 3.7 58.0 + - + +
43B ILE* 4.2 12.6 - - + -
44B PHE* 4.8 0.2 - - + -
128B ILE* 4.4 12.1 - - + -
140B SER* 2.9 33.8 + - - +
142B TYR* 1.3 79.3 - - - +
144B VAL* 1.3 63.0 + - + +
191B LYS* 3.4 16.8 + - - +
194B GLN* 4.1 2.6 + - - +
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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