Contacts of the helix formed by residues 148 - 162 (chain F) in PDB entry 3V3K
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 148 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E GLY* 3.2 32.1 - - - -
177E ARG* 5.0 1.6 - - - -
144F PRO* 3.6 11.5 - - - +
145F HIS* 2.8 28.0 + - - -
146F HIS 3.4 0.2 - - - -
147F SER* 1.3 83.9 + - - +
149F GLU* 1.3 64.5 + - - +
150F LEU* 3.7 3.6 + - - -
151F TYR* 3.2 17.3 + - - +
152F GLY 3.6 12.0 + - - -
181F TYR* 3.7 10.2 - - - -
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E GLY 4.4 2.9 - - - -
177E ARG* 5.4 6.9 - - + +
77F MET* 4.7 10.9 - - - +
80F ARG* 3.6 49.3 + - - +
81F ASN* 3.8 23.4 + - - +
148F SER* 1.3 73.8 - - - +
150F LEU* 1.3 63.5 + - - +
152F GLY* 3.2 12.8 + - - -
153F ASP* 3.3 9.4 + - - +
178F ASP 5.0 0.9 - - - +
181F TYR* 5.2 4.2 - - - +
183F LYS* 2.9 32.0 + - - +
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F VAL* 3.7 31.2 - - + -
76F LEU* 4.0 19.5 - - + -
110F TYR* 4.9 2.0 - - - +
114F LEU* 4.0 11.9 - - + -
117F LEU* 3.9 27.1 - - + -
141F LEU 4.6 7.4 - - - +
142F LEU* 6.2 0.2 - - - -
144F PRO* 4.1 18.6 - - + -
148F SER* 3.4 4.8 + - - +
149F GLU* 1.3 75.6 - - - +
151F TYR* 1.3 60.5 + - - +
153F ASP* 4.6 4.0 - - - -
154F LEU* 3.0 44.3 + - + +
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Residues in contact with TYR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E GLU* 3.2 48.7 + - - +
290E LYS* 5.4 1.8 - - - -
144F PRO* 3.7 29.1 - - + +
145F HIS 3.3 19.1 - - - +
146F HIS* 3.5 24.0 - - + -
148F SER* 3.2 11.6 + - - +
149F GLU 3.3 0.2 - - - -
150F LEU* 1.3 76.1 - - - +
152F GLY* 1.3 59.9 + - - +
154F LEU* 3.4 3.3 + - + +
155F ARG* 2.9 61.1 + - + +
181F TYR* 3.3 28.7 - + - -
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Residues in contact with GLY 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F SER 3.6 4.4 + - - -
149F GLU 3.2 7.1 + - - -
151F TYR* 1.3 80.7 - - - +
153F ASP* 1.3 59.8 + - - +
155F ARG* 4.0 5.2 + - - +
156F ALA* 3.1 27.0 + - - +
178F ASP* 3.7 9.5 - - - +
181F TYR* 3.7 34.5 - - - -
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Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 2.8 28.7 + - - -
110F TYR* 2.7 30.2 + - - -
114F LEU* 3.7 25.2 - - + +
149F GLU 3.3 5.4 + - - +
150F LEU* 3.9 6.3 - - - +
151F TYR 3.3 0.2 - - - -
152F GLY* 1.3 76.1 - - - +
154F LEU* 1.3 53.5 + - - +
156F ALA* 3.4 6.2 + - - +
157F MET* 2.8 36.6 + - - +
176F VAL 4.2 0.7 - - - +
177F PRO* 4.1 6.9 - - - +
178F ASP 2.9 29.9 + - - +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU* 4.2 17.7 - - + +
117F LEU* 4.0 28.5 - - + -
118F HIS* 4.2 20.2 - - + +
121F LYS* 5.4 11.4 - - + +
142F LEU* 4.2 14.1 - - - +
144F PRO* 4.1 20.2 - - + -
150F LEU* 3.0 44.8 + - + +
151F TYR* 4.0 3.6 - - + +
153F ASP* 1.3 73.1 - - - +
155F ARG* 1.3 60.3 + - - +
157F MET* 3.4 5.0 + - + +
158F LYS* 3.0 28.8 + - - +
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Residues in contact with ARG 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E LYS* 5.0 7.5 - - - +
151F TYR* 2.9 46.6 + - + +
152F GLY 4.0 4.3 + - - +
154F LEU* 1.3 76.4 - - - +
156F ALA* 1.3 60.5 + - - +
158F LYS* 3.6 10.8 + - + +
159F CYS* 3.3 37.6 + - - -
167F ASP* 4.2 21.3 + - - +
168F PHE* 4.3 24.4 - - - -
178F ASP* 4.6 7.7 + - - -
181F TYR* 3.7 35.3 + - - -
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F GLY 3.1 21.0 + - - +
153F ASP* 3.6 5.8 - - - +
155F ARG* 1.3 75.4 - - - +
157F MET* 1.3 63.5 + - - +
159F CYS* 3.2 13.6 + - - +
160F LEU* 3.3 19.9 + - - +
174F ILE* 3.9 16.3 - - + +
175F ARG 3.2 27.4 - - - +
176F VAL* 4.6 3.1 - - - -
178F ASP* 4.3 7.9 - - + +
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Residues in contact with MET 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 4.3 9.9 - - - -
111F ILE* 4.6 5.8 - - - -
114F LEU* 3.4 36.3 - - + +
115F PHE* 3.4 46.4 - - + -
118F HIS* 3.9 19.7 - - + -
153F ASP 2.8 14.9 + - - +
154F LEU* 3.4 9.2 + - + +
156F ALA* 1.3 70.9 - - - +
158F LYS* 1.3 63.1 + - - +
160F LEU* 3.5 1.8 + - - +
161F VAL* 3.1 52.4 + - + +
176F VAL* 4.0 24.4 + - + -
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Residues in contact with LYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F HIS* 3.9 17.9 - - + +
121F LYS* 6.0 2.2 - - - +
125F GLU* 5.5 6.7 + - - -
154F LEU 3.0 17.2 + - - +
155F ARG* 3.6 12.1 - - + +
156F ALA 3.3 0.2 - - - -
157F MET* 1.3 76.2 - - - +
159F CYS* 1.3 57.3 + - - +
162F GLU* 3.0 64.8 + - + +
165F SER* 4.7 17.0 - - - +
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Residues in contact with CYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ARG* 3.3 29.8 - - - -
156F ALA* 3.2 10.4 + - - +
158F LYS* 1.3 79.2 - - - +
160F LEU* 1.3 58.0 - - - +
163F GLY* 3.1 9.2 + - - -
164F CYS* 2.9 49.2 + - - +
165F SER* 3.5 15.0 - - - +
167F ASP* 5.5 2.2 - - - -
174F ILE* 3.4 31.6 - - + -
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F VAL 4.2 1.6 - - - +
30F SER 3.2 33.0 - - - +
31F GLU* 5.2 0.9 - - - -
32F LEU* 4.1 25.0 - - + +
156F ALA 3.3 12.8 + - - +
157F MET 4.2 2.5 - - - +
159F CYS* 1.3 77.3 - - + +
161F VAL* 1.3 65.8 + - - +
163F GLY* 4.2 3.1 + - - -
174F ILE* 4.2 25.6 - - + +
175F ARG 5.0 0.2 - - - -
176F VAL* 3.4 44.6 - - + +
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.6 19.5 - - + -
115F PHE* 4.0 15.9 - - + -
118F HIS* 3.7 23.3 - - + +
157F MET* 3.1 42.6 + - + +
160F LEU* 1.3 78.8 - - - +
162F GLU* 1.3 64.4 + - + +
163F GLY* 3.3 2.2 + - - -
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Residues in contact with GLU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F HIS* 3.9 21.4 + - + +
122F VAL* 4.1 16.3 - - - +
158F LYS* 3.0 50.0 + - + +
161F VAL* 1.3 77.8 - - + +
163F GLY* 1.3 65.1 + - - +
165F SER* 5.3 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