Contacts of the helix formed by residues 136 - 144 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN 4.5 1.4 + - - -
12C GLY* 3.8 27.5 - - - +
105C THR* 3.0 36.9 - - + +
106C GLU* 2.9 15.8 + - - +
107C ALA* 3.9 28.6 - - - +
108C PRO* 4.8 0.7 - - + -
134C ALA 3.6 0.2 + - - -
135C ILE* 1.3 73.6 - - - +
137C ALA* 1.3 63.7 + - - +
139C LEU* 3.3 13.1 + - - +
140C SER 3.3 8.5 + - - -
153C ASP* 2.9 31.6 - - - +
158C VAL 5.4 0.3 - - - +
160C HIS* 4.3 3.3 + - - -
338C VAL* 3.8 22.3 - - + +
401C ADP 4.4 1.2 + - - -
402C MG 3.9 10.2 - - - -
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PRO* 5.2 2.8 - - + +
135C ILE* 3.3 4.3 - - + +
136C GLN* 1.3 79.7 - - - +
138C VAL* 1.3 63.8 + - - +
140C SER* 2.6 23.4 + - - -
141C LEU* 3.0 5.9 + - - +
151C VAL* 3.7 29.6 - - + +
153C ASP* 4.5 14.6 + - + +
160C HIS* 5.9 0.2 - - + -
162C VAL* 3.9 35.2 - - + +
299C SER* 5.5 0.2 - - - -
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE* 3.2 26.9 - - + +
136C GLN 3.4 0.2 - - - -
137C ALA* 1.3 76.3 - - - +
139C LEU* 1.3 69.7 + - + +
141C LEU* 3.0 14.0 + - + +
142C TYR* 2.9 49.5 + - + -
151C VAL* 5.8 0.2 - - - -
162C VAL* 5.0 6.3 - - + -
164C ILE* 3.9 27.8 - - + -
345C LEU* 5.8 1.6 - - + -
374C PHE* 5.7 3.8 - - + -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 5.6 1.8 - - + -
103C LEU* 4.2 11.0 - - + -
105C THR* 4.2 20.9 - - - +
134C ALA* 3.7 22.9 - - + -
135C ILE 3.2 15.3 - - - +
136C GLN 3.3 9.1 + - - +
137C ALA 3.1 0.4 - - - -
138C VAL* 1.3 82.3 - - + +
140C SER* 1.3 59.6 + - - +
142C TYR* 3.1 7.1 + - + +
143C ALA 2.9 23.4 + - - -
337C SER 4.3 0.4 - - - -
338C VAL* 3.6 25.8 - - + +
341C GLY* 3.1 16.7 - - - +
342C GLY* 3.6 23.3 - - - +
345C LEU* 4.4 15.7 - - + -
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLN 3.3 6.4 + - - -
137C ALA 2.6 19.8 + - - -
139C LEU* 1.3 79.8 - - - +
141C LEU* 1.3 63.0 + - - +
143C ALA* 3.1 3.1 + - - +
144C SER* 2.9 26.0 + - - -
151C VAL* 3.2 19.9 - - - +
297C VAL* 4.6 4.4 - - - +
299C SER* 3.7 25.8 - - - -
337C SER* 3.7 25.5 + - - -
338C VAL* 4.3 3.1 - - - +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA 3.0 6.4 + - - +
138C VAL* 3.0 18.9 + - + +
140C SER* 1.3 80.7 + - - +
142C TYR* 1.3 65.8 + - + +
144C SER* 3.2 13.9 + - - -
145C GLY 3.2 8.1 + - - -
146C ARG* 3.2 33.5 + - + +
147C THR* 4.0 6.7 - - - +
148C THR 4.0 24.5 - - - +
149C GLY* 4.2 2.9 - - - +
151C VAL* 3.9 21.1 - - + -
164C ILE* 3.2 36.3 - - + -
167C GLY* 5.8 2.0 - - - -
297C VAL* 4.8 7.6 - - + -
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Residues in contact with TYR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL* 2.9 48.0 + - + -
139C LEU* 3.2 9.9 - - - +
141C LEU* 1.3 81.7 - - + +
143C ALA* 1.3 55.0 + - - +
145C GLY* 2.7 24.8 + - - +
146C ARG 4.8 2.5 - - - -
341C GLY* 4.3 0.9 - - - -
344C ILE* 3.8 36.5 - - + +
345C LEU* 3.3 35.8 - - + +
348C LEU* 4.7 15.5 - - + +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU 2.9 7.2 + - - +
140C SER 3.1 7.8 + - - +
142C TYR* 1.3 76.8 - - - +
144C SER* 1.3 60.3 + - - +
145C GLY* 3.4 0.7 + - - -
337C SER* 3.3 34.3 - - - +
340C ILE* 3.8 23.0 - - + +
341C GLY* 3.7 11.4 - - - +
344C ILE* 5.0 3.4 - - - -
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C SER 2.9 14.2 + - - -
141C LEU* 3.6 11.0 - - - -
142C TYR 3.1 0.4 - - - -
143C ALA* 1.3 74.9 - - - +
145C GLY* 1.3 63.0 + - - +
146C ARG* 3.4 27.0 + - - +
297C VAL* 3.8 19.4 - - - +
329C ILE* 5.5 6.7 - - - +
331C PRO* 4.3 17.6 - - - +
337C SER* 5.3 2.9 + - - -
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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