Contacts of the helix formed by residues 136 - 145 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN 4.5 0.8 + - - -
12A GLY* 3.7 27.5 - - - +
105A THR* 2.9 35.3 - - + +
106A GLU* 2.9 16.0 + - - +
107A ALA* 3.9 29.0 - - - +
108A PRO* 4.7 0.9 - - + +
134A ALA 3.6 0.2 + - - -
135A ILE* 1.3 74.0 - - - +
137A ALA* 1.3 64.7 + - - +
139A LEU* 3.3 12.9 + - - +
140A SER* 3.3 7.8 + - - -
153A ASP* 3.0 30.5 - - - +
158A VAL 5.4 0.2 - - - +
160A HIS* 4.3 3.1 + - - -
338A VAL* 3.8 21.6 - - + +
401A ADP 4.3 1.2 + - - -
402A MG 3.9 10.9 - - - -
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Residues in contact with ALA 137 (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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108A PRO* 5.2 2.2 - - + +
135A ILE* 3.3 4.9 - - + +
136A GLN* 1.3 79.3 - - - +
138A VAL* 1.3 63.1 + - - +
140A SER* 2.6 25.0 + - - -
141A LEU* 3.0 5.4 + - - +
151A VAL* 3.7 30.1 - - + +
153A ASP* 4.5 12.9 + - + +
160A HIS* 5.9 0.4 - - + -
162A VAL* 3.9 34.5 - - + -
299A SER* 5.5 0.2 - - - -
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Residues in contact with VAL 138 (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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135A ILE* 3.2 27.8 - - + +
137A ALA* 1.3 75.5 - - - +
139A LEU* 1.3 71.2 + - + +
141A LEU* 3.0 12.2 + - - +
142A TYR* 2.9 49.2 + - + -
162A VAL* 5.0 6.7 - - + -
164A ILE* 3.9 27.4 - - + -
345A LEU* 5.8 1.6 - - + -
374A PHE* 5.7 1.8 - - + -
42C VAL* 4.0 27.6 - - + +
43C MET* 4.2 5.2 - - - -
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Residues in contact with LEU 139 (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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8A VAL* 5.6 1.3 - - + -
103A LEU* 4.2 10.8 - - + -
105A THR* 4.1 21.8 - - - +
134A ALA* 3.7 21.5 - - + -
135A ILE 3.2 15.5 - - - +
136A GLN 3.3 8.9 + - - +
137A ALA 3.1 0.4 - - - -
138A VAL* 1.3 85.2 - - + +
140A SER* 1.3 58.5 - - - +
142A TYR* 3.1 8.6 + - + +
143A ALA 2.9 23.6 + - - -
337A SER 4.3 0.2 - - - -
338A VAL* 3.6 27.4 - - + +
341A GLY* 3.1 16.4 - - - +
342A GLY* 3.6 23.6 - - - +
345A LEU* 4.5 13.0 - - + -
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Residues in contact with SER 140 (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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136A GLN 3.3 7.3 + - - -
137A ALA 2.6 18.1 + - - -
139A LEU* 1.3 77.4 - - - +
141A LEU* 1.3 63.5 + - - +
143A ALA* 3.1 2.8 + - - +
144A SER* 2.9 26.1 + - - -
151A VAL* 3.2 18.4 - - - +
297A VAL* 4.5 4.3 - - - +
299A SER* 3.7 26.0 - - - -
337A SER* 3.7 26.8 + - - -
338A VAL* 4.3 2.4 - - - +
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Residues in contact with LEU 141 (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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137A ALA 3.0 6.2 + - - +
138A VAL* 3.0 10.6 + - - +
140A SER* 1.3 83.6 + - - +
142A TYR* 1.3 61.0 + - - +
144A SER* 3.2 13.7 + - - -
145A GLY 3.2 7.6 + - - -
146A ARG* 3.1 31.0 + - + +
147A THR 4.0 2.2 - - - +
148A THR 4.0 24.0 - - - +
149A GLY* 4.2 2.5 - - - +
151A VAL* 3.9 20.4 - - + -
164A ILE* 3.3 32.8 - - + -
297A VAL* 4.8 7.2 - - + -
43C MET* 3.6 35.0 - - + -
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Residues in contact with TYR 142 (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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138A VAL* 2.9 48.1 + - + -
139A LEU* 3.2 10.1 - - - +
141A LEU* 1.3 76.5 - - - +
143A ALA* 1.3 57.8 + - - +
145A GLY* 2.7 24.9 + - - +
146A ARG 4.8 2.7 - - - -
341A GLY* 4.3 0.7 - - - -
344A ILE* 3.7 33.9 - - + +
345A LEU* 3.3 32.4 - - + +
348A LEU* 4.7 4.5 - - + -
43C MET* 2.9 21.3 - - + +
44C VAL* 2.3 39.0 + - - +
560F PHE* 3.6 26.0 - + - -
561F PRO* 4.0 17.3 - - + +
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Residues in contact with ALA 143 (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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139A LEU 2.9 2.8 + - - +
140A SER 3.4 7.6 - - - +
142A TYR* 1.3 81.1 - - - +
144A SER* 1.3 59.5 + - - +
145A GLY* 3.4 0.7 + - - -
337A SER* 3.3 34.3 - - - +
340A ILE* 3.9 21.8 - - + +
341A GLY* 3.7 12.6 - - - +
344A ILE* 5.0 2.9 - - - -
435F GLN* 5.9 0.9 + - - -
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Residues in contact with SER 144 (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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140A SER 2.9 14.8 + - - -
141A LEU* 3.6 11.0 - - - -
142A TYR 3.1 0.6 - - - -
143A ALA* 1.3 75.7 - - - +
145A GLY* 1.3 61.5 + - - +
146A ARG* 3.4 26.0 + - - +
297A VAL* 3.8 18.5 - - - +
329A ILE* 5.5 6.6 - - - +
331A PRO* 4.3 17.2 - - - +
337A SER* 5.3 2.9 + - - -
387F ASP* 5.4 3.8 - - - +
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Residues in contact with GLY 145 (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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141A LEU 3.2 0.6 + - - -
142A TYR 2.7 17.9 + - - -
143A ALA 3.1 1.1 - - - -
144A SER* 1.3 78.6 - - - +
146A ARG* 1.3 56.4 + - - +
435F GLN* 6.2 1.8 - - - -
559F TRP 5.7 1.6 - - - -
561F PRO* 3.2 27.3 - - - +
562F LYS* 3.0 21.3 + - - -
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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