Contacts of the helix formed by residues 136 - 144 (chain B) in PDB entry 5JLH
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 GLN 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASN 4.5 1.4 + - - -
12B GLY* 3.8 27.1 - - - +
105B THR* 3.0 36.4 - - + +
106B GLU* 2.9 16.4 + - - +
107B ALA* 3.9 28.3 - - - +
108B PRO* 4.8 0.4 - - + -
134B ALA 3.6 0.2 + - - -
135B ILE* 1.3 74.0 - - - +
137B ALA* 1.3 63.3 - - - +
139B LEU* 3.3 12.9 + - - +
140B SER 3.3 8.5 + - - -
153B ASP* 2.9 31.6 - - - +
158B VAL 5.3 0.2 - - - +
160B HIS* 4.3 3.3 + - - -
338B VAL* 3.8 21.8 - - + +
401B ADP 4.4 1.3 + - - -
402B MG 3.9 10.6 - - - -
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Residues in contact with ALA 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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108B PRO* 5.2 3.0 - - + +
135B ILE* 3.3 4.1 - - + +
136B GLN* 1.3 79.7 - - - +
138B VAL* 1.3 62.9 + - - +
140B SER* 2.6 23.2 + - - -
141B LEU* 3.0 5.9 + - - +
151B VAL* 3.7 31.3 - - + +
153B ASP* 4.5 12.1 - - + +
160B HIS* 5.9 0.2 - - + -
161B THR 5.6 0.2 - - - -
162B VAL* 3.9 34.5 - - + -
299B SER* 5.4 0.2 - - - -
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Residues in contact with VAL 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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42A VAL* 4.0 26.5 - - + +
43A MET* 4.1 5.6 - - - -
135B ILE* 3.2 27.3 - - + +
136B GLN 3.4 0.2 - - - -
137B ALA* 1.3 75.2 - - - +
139B LEU* 1.3 70.4 + - + +
141B LEU* 3.0 11.1 + - - +
142B TYR* 2.9 48.9 + - + -
151B VAL* 5.8 0.2 - - - -
162B VAL* 5.0 6.3 - - + -
164B ILE* 3.9 27.1 - - + -
345B LEU* 5.8 1.6 - - + -
374B PHE* 5.7 2.5 - - + -
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Residues in contact with LEU 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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8B VAL* 5.6 1.6 - - + -
103B LEU* 4.2 10.8 - - + -
105B THR* 4.2 21.5 - - - +
134B ALA* 3.7 22.2 - - + -
135B ILE 3.2 15.5 - - - +
136B GLN 3.3 9.6 + - - +
137B ALA 3.1 0.4 - - - -
138B VAL* 1.3 82.2 - - + +
140B SER* 1.3 59.3 - - - +
142B TYR* 3.1 7.3 + - + +
143B ALA 2.9 22.9 + - - -
337B SER 4.3 0.2 - - - -
338B VAL* 3.6 26.2 - - + +
341B GLY* 3.1 17.1 - - - +
342B GLY* 3.6 23.6 - - - +
345B LEU* 4.4 15.5 - - + -
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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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136B GLN 3.3 6.4 + - - -
137B ALA 2.6 19.6 + - - -
139B LEU* 1.3 79.2 - - - +
141B LEU* 1.3 61.9 + - - +
143B ALA* 3.1 3.1 + - - +
144B SER* 2.9 25.7 + - - -
151B VAL* 3.2 19.8 - - - +
297B VAL* 4.6 4.6 - - - +
299B SER* 3.7 25.6 - - - -
337B SER* 3.7 25.7 + - - -
338B VAL* 4.3 2.9 - - - +
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Residues in contact with LEU 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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43A MET* 3.6 35.9 - - + -
137B ALA 3.0 6.2 + - - +
138B VAL* 3.0 10.4 + - - +
140B SER* 1.3 82.6 + - - +
142B TYR* 1.3 61.9 + - - +
144B SER* 3.2 14.2 + - - -
145B GLY 3.2 7.8 + - - -
146B ARG* 3.2 29.7 + - + +
147B THR 4.0 2.0 - - - +
148B THR 4.0 23.6 - - - +
149B GLY* 4.2 3.8 - - - +
151B VAL* 3.9 19.7 - - + -
164B ILE* 3.2 31.6 - - + -
297B VAL* 4.8 7.4 - - + -
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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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43A MET* 2.9 24.6 - - + +
44A VAL* 2.2 49.0 + - - +
138B VAL* 2.9 48.9 + - + -
139B LEU* 3.2 10.1 - - - +
141B LEU* 1.3 77.7 - - - +
143B ALA* 1.3 55.6 + - - +
145B GLY* 2.7 25.2 + - - +
146B ARG 4.8 3.1 - - - -
341B GLY* 4.3 0.9 - - - -
344B ILE* 3.8 36.4 - - + +
345B LEU* 3.2 32.2 - - + +
348B LEU* 4.7 9.2 - - + -
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Residues in contact with ALA 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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139B LEU 2.9 2.8 + - - +
140B SER 3.1 8.0 + - - +
142B TYR* 1.3 80.9 - - - +
144B SER* 1.3 59.9 + - - +
145B GLY* 3.4 0.7 + - - -
337B SER* 3.3 34.8 - - - +
340B ILE* 3.8 21.4 - - + +
341B GLY* 3.7 13.0 - - - +
344B ILE* 5.0 3.1 - - - -
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Residues in contact with SER 144 (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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140B SER 2.9 13.5 + - - -
141B LEU* 3.6 9.0 - - - -
142B TYR 3.1 0.4 - - - -
143B ALA* 1.3 75.2 - - - +
145B GLY* 1.3 62.9 + - - +
146B ARG* 3.3 26.7 + - - +
297B VAL* 3.8 20.4 - - - +
329B ILE* 5.5 6.7 - - - +
331B PRO* 4.3 17.4 - - - +
337B SER* 5.3 2.8 + - - -
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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