Contacts of the helix formed by residues 144 - 153 (chain B) in PDB entry 3VF0
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 THR 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ARG* 5.8 6.3 - - - +
142B SER 3.8 11.0 - - - +
143B LEU* 1.4 74.4 - - - +
145B GLN* 1.4 63.3 + - - +
146B GLN* 3.5 9.2 + - - +
147B GLN* 3.1 39.5 + - - +
148B PHE* 3.0 22.0 + - - +
163B LEU* 3.6 3.1 - - - -
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Residues in contact with GLN 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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50B HIS* 3.8 15.0 + - + -
51B THR* 4.8 1.2 + - - -
144B THR* 1.4 72.6 - - - +
146B GLN* 1.4 57.9 + - - +
148B PHE* 3.2 5.1 + - - +
149B GLU* 3.0 55.6 + - - +
161B CYS* 3.0 28.6 + - - -
162B PHE* 3.4 2.7 - - - +
163B LEU* 2.9 42.1 + - - +
165B TYR* 3.5 9.6 + - - +
3011B GOL 3.5 38.1 + - - +
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Residues in contact with GLN 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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144B THR* 3.2 9.2 + - - +
145B GLN* 1.4 78.2 - - - +
147B GLN* 1.4 56.9 + - + +
149B GLU* 3.2 26.1 + - - +
150B GLU* 3.1 52.5 + - - +
153B ARG* 4.4 7.8 + - - -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B SER 4.0 2.6 - - - +
143B LEU* 3.5 29.2 - - + +
144B THR* 3.1 43.9 + - - +
146B GLN* 1.4 73.0 - - + +
148B PHE* 1.3 59.8 + - - +
150B GLU* 3.4 21.1 + - - +
151B LEU* 3.1 26.5 + - - +
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Residues in contact with PHE 148 (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 VAL* 3.9 19.5 - - + -
139B LEU* 3.6 37.9 - - + -
143B LEU* 3.9 11.1 - - + +
144B THR 3.0 11.3 + - - +
145B GLN* 3.2 10.1 + - - +
147B GLN* 1.3 75.1 - - - +
149B GLU* 1.3 62.9 + - - +
151B LEU* 3.4 8.0 + - + +
152B VAL* 3.2 39.4 + - + +
161B CYS* 3.7 20.0 - - - -
162B PHE 3.8 15.3 - - - -
163B LEU* 3.8 17.3 - - + -
176B GLY* 3.6 22.0 - - - -
177B PHE 3.6 23.8 - - - -
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Residues in contact with GLU 149 (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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50B HIS* 4.1 8.5 + - - -
145B GLN* 3.0 39.8 + - - +
146B GLN* 3.4 32.1 + - - +
148B PHE* 1.3 75.8 - - - +
150B GLU* 1.3 56.0 + - - +
152B VAL* 4.0 0.2 - - - +
153B ARG* 2.9 41.6 + - + +
158B LEU* 5.1 3.4 - - + -
161B CYS* 3.6 26.5 - - - -
3005B GOL 3.9 24.0 + - - +
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Residues in contact with GLU 150 (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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146B GLN* 3.1 32.1 + - - +
147B GLN* 3.5 23.3 - - - +
148B PHE 3.3 0.4 - - - -
149B GLU* 1.3 76.8 - - - +
151B LEU* 1.3 60.3 + - - +
153B ARG* 3.7 37.7 + - - +
154B PRO* 3.5 17.0 - - - +
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Residues in contact with LEU 151 (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 VAL* 4.4 3.8 - - + -
139B LEU* 3.8 28.9 - - + -
143B LEU* 4.7 3.1 - - + -
147B GLN 3.1 13.6 + - - +
148B PHE* 3.5 12.8 - - + +
149B GLU 3.3 0.2 - - - -
150B GLU* 1.3 76.6 - - - +
152B VAL* 1.4 70.2 + - + +
154B PRO* 3.6 5.7 - - - +
155B PHE* 3.5 19.8 - - - -
193B LEU* 3.8 22.3 - - + +
196B LYS* 4.2 18.2 - - + -
198B LEU* 4.2 19.1 - - + -
203B LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 152 (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 VAL* 4.3 3.6 - - + -
148B PHE* 3.2 39.9 + - + +
149B GLU 4.0 1.8 - - - +
151B LEU* 1.4 81.6 - - + +
153B ARG* 1.3 66.1 + - - +
154B PRO* 3.4 3.6 - - - -
155B PHE* 3.5 8.4 - - - -
158B LEU* 4.0 7.2 - - + -
161B CYS* 3.7 25.4 - - - -
178B ALA* 3.9 17.7 - - + -
180B TYR* 2.5 37.8 + - - +
193B LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 153 (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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146B GLN* 4.4 7.7 + - - -
149B GLU* 2.9 23.9 + - + +
150B GLU* 3.7 38.3 + - - +
152B VAL* 1.3 73.4 - - - +
154B PRO* 1.4 76.6 - - + +
155B PHE 3.2 3.1 - - - -
156B GLY 3.0 19.4 + - - +
158B LEU* 3.9 20.0 - - + -
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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