Contacts of the helix formed by residues 137 - 146 (chain B) in PDB entry 2V5Q
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 SER 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ARG 4.5 1.9 - - - +
136B ARG* 1.3 81.3 - - - +
138B LEU* 1.3 66.4 + - - +
139B LEU* 3.2 9.2 + - - +
140B GLU* 2.7 29.5 + - - +
141B LEU* 3.4 10.9 + - - +
179B LEU 3.5 7.0 - - - -
180B GLY* 3.5 25.7 + - - -
182B LEU 3.1 17.9 - - - -
183B PHE* 3.9 6.5 - - - +
184B LEU* 4.2 7.8 - - - +
79C TYR* 4.6 1.0 + - - -
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Residues in contact with LEU 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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137B SER* 1.3 70.2 - - - +
139B LEU* 1.3 59.6 + - - +
140B GLU 3.4 0.2 - - - -
141B LEU* 3.8 13.6 - - + +
142B HIS* 2.7 32.0 + - - +
156B TYR* 4.0 33.2 - - + -
160B ILE* 4.0 19.5 - - + -
179B LEU* 3.3 27.5 + - + +
182B LEU* 2.9 28.9 + - + +
184B LEU* 3.8 24.7 - - + -
190B VAL* 3.8 17.0 - - + -
244B LEU* 4.7 10.4 - - + +
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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
----------------------------------------------------------
137B SER* 3.1 12.2 - - - +
138B LEU* 1.3 77.3 - - - +
140B GLU* 1.3 67.2 + - - +
142B HIS* 3.2 9.4 + - + +
143B LYS* 2.8 67.9 + - + +
179B LEU* 3.4 25.5 + - + +
180B GLY* 3.7 19.1 - - - +
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Residues in contact with GLU 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 ARG* 3.4 16.6 - - + +
137B SER* 2.7 39.9 + - - +
139B LEU* 1.3 91.3 - - - +
141B LEU* 1.3 63.9 + - - +
143B LYS* 3.3 9.6 + - + +
144B ARG* 3.2 28.2 + - - +
46C THR* 3.9 16.3 - - + +
78C VAL* 4.2 20.0 - - + -
79C TYR* 3.5 20.9 - - + +
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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
----------------------------------------------------------
137B SER 3.4 11.0 + - - +
138B LEU* 3.8 16.4 - - + +
139B LEU 3.2 0.4 - - - -
140B GLU* 1.3 79.7 - - - +
142B HIS* 1.3 59.5 + - + +
144B ARG* 3.2 1.9 + - - -
145B ARG* 2.8 36.3 + - + +
148B LEU* 3.6 38.4 - - + -
156B TYR* 3.9 28.7 - - + +
184B LEU* 4.0 6.5 - - + -
244B LEU* 5.5 1.8 - - + -
318B CYS* 3.9 19.5 - - - +
319B LEU* 3.9 28.7 - - + -
79C TYR* 3.5 11.3 + - - +
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Residues in contact with HIS 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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138B LEU 2.7 23.6 + - - +
139B LEU* 3.5 11.0 - - + +
141B LEU* 1.3 77.4 - - - +
143B LYS* 1.3 67.7 + - + +
146B LYS* 2.7 57.1 + - + +
148B LEU* 5.9 0.2 - - - -
179B LEU* 3.6 22.2 - - + -
243B THR* 3.5 27.3 + - + +
244B LEU* 5.1 7.7 - - + +
247B GLY* 3.1 30.2 + - - -
248B LYS* 4.8 1.1 - - - -
249B PRO* 5.5 4.2 - - - +
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Residues in contact with LYS 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* 2.8 58.5 + - + +
140B GLU* 3.6 12.6 + - + +
141B LEU 3.3 0.2 - - - -
142B HIS* 1.3 79.4 - - + +
144B ARG* 1.3 61.0 + - - +
146B LYS* 4.2 19.6 - - - +
23C ARG* 5.8 0.9 + - - -
45C ASN* 3.7 48.6 + - - +
46C THR* 3.9 18.4 - - + -
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Residues in contact with ARG 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 GLU 3.2 14.5 + - - +
141B LEU 3.8 1.1 - - - +
142B HIS 3.2 0.4 - - - -
143B LYS* 1.3 78.5 - - - +
145B ARG* 1.3 62.2 + - - +
146B LYS* 5.3 1.5 - - - +
319B LEU 2.9 22.7 - - - +
320B THR* 3.0 41.0 + - - +
23C ARG* 3.3 28.5 + - - +
44C ASP* 5.7 0.9 - - - +
46C THR* 3.0 29.4 + - + +
48C LEU* 3.4 21.5 - - + +
77C ASP* 2.2 49.3 + - - +
79C TYR* 3.4 29.7 - - - -
81C PHE* 4.3 2.4 - - - -
86C LEU* 5.1 0.6 - - - +
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Residues in contact with ARG 145 (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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141B LEU* 2.8 19.4 + - + +
144B ARG* 1.3 79.9 - - - +
146B LYS* 1.3 69.7 + - - +
147B ALA 3.3 12.5 + - - +
148B LEU* 3.7 35.3 - - + +
149B THR* 4.1 2.8 - - - +
152B GLU* 2.9 41.0 + - - -
318B CYS* 2.8 40.1 + - - +
319B LEU 4.2 5.6 - - - +
320B THR 3.5 4.7 - - - -
321B ILE* 3.4 41.2 + - - +
322B PRO* 3.5 24.2 - - - +
323B PRO* 4.0 0.2 - - - +
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Residues in contact with LYS 146 (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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142B HIS* 2.7 51.5 + - + +
143B LYS* 4.2 17.0 + - - +
144B ARG 5.3 1.1 - - - +
145B ARG* 1.3 75.2 - - - +
147B ALA* 1.3 66.2 + - - +
148B LEU* 3.2 12.5 + - - +
243B THR 4.8 0.3 - - - +
244B LEU* 4.3 3.1 - - - +
247B GLY* 4.0 24.8 + - - +
248B LYS* 6.1 1.4 - - - +
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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