Contacts of the helix formed by residues 156 - 167 (chain A) in PDB entry 3VVK
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 ASP 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR* 2.5 28.1 + - - -
132A PRO* 3.4 13.3 - - - +
135A LEU* 3.4 18.2 - - + -
152A ALA 3.0 21.3 + - - +
153A ILE 3.7 3.8 - - - +
154A THR 3.2 0.2 - - - -
155A PHE* 1.3 73.1 - - - +
157A ILE* 1.3 67.8 + - - +
159A MET* 3.2 18.5 + - - +
160A CYS* 3.1 21.3 + - - -
190A VAL* 3.7 11.0 - - + +
222A TRP* 3.2 27.7 - - - -
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Residues in contact with ILE 157 (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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128A ALA* 4.3 12.1 - - + +
132A PRO* 3.7 22.4 - - + -
153A ILE* 3.0 34.1 + - + +
154A THR* 3.5 4.5 - - - +
156A ASP* 1.3 73.4 - - - +
158A ALA* 1.3 61.3 + - - +
160A CYS* 3.0 7.0 + - - +
161A VAL* 2.8 42.6 + - + +
302D L3P 4.1 53.2 - - + -
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Residues in contact with ALA 158 (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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154A THR 2.9 13.6 + - - +
155A PHE* 3.2 13.4 + - + +
157A ILE* 1.3 76.7 - - - +
159A MET* 1.3 62.3 + - - +
161A VAL* 3.9 0.3 - - - +
162A THR* 2.9 31.5 + - + +
186A CYS* 3.6 17.5 - - - -
73B LEU* 5.7 1.8 - - + -
76B VAL* 4.7 9.4 - - + -
302D L3P 4.1 32.3 - - + +
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Residues in contact with MET 159 (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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131A THR* 5.0 0.4 - - + -
155A PHE 2.8 13.0 + - - +
156A ASP* 3.2 39.0 - - - +
158A ALA* 1.3 77.4 - - - +
160A CYS* 1.3 68.2 + - - +
162A THR* 3.3 1.2 + - - -
163A GLY* 3.1 15.1 + - - -
183A SER* 2.7 42.3 + - - +
186A CYS* 3.7 14.5 - - + +
187A PHE* 3.6 37.0 - - - +
190A VAL* 5.1 2.7 - - - -
222A TRP* 4.4 2.2 - - + -
301A RET 3.5 43.4 - - + +
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Residues in contact with CYS 160 (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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124A TYR* 3.9 11.7 - - + +
127A TRP* 3.6 13.9 - - + -
128A ALA* 3.5 40.8 - - + +
131A THR* 3.6 18.4 - - - -
156A ASP* 3.1 16.5 + - - +
157A ILE 3.0 7.6 + - - +
159A MET* 1.3 87.8 - - - +
161A VAL* 1.3 61.0 + - - +
163A GLY* 3.2 1.9 + - - -
164A LEU* 3.0 28.1 + - - +
301A RET 5.1 6.7 - - - -
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Residues in contact with VAL 161 (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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128A ALA* 5.2 6.7 - - + -
157A ILE* 2.8 33.8 + - + +
158A ALA 4.0 0.9 - - - +
160A CYS* 1.3 75.2 - - + +
162A THR* 1.3 59.6 + - + +
164A LEU* 3.3 14.4 + - + +
165A ALA* 2.9 27.8 + - + +
179A TRP* 6.6 0.2 - - + -
80B ALA* 6.4 1.1 - - + -
302D L3P 3.6 32.3 - - + -
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Residues in contact with THR 162 (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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158A ALA* 2.9 23.2 + - + +
159A MET 3.3 0.5 + - - -
161A VAL* 1.3 77.7 - - + +
163A GLY* 1.3 63.0 + - - +
165A ALA* 3.6 6.9 - - - +
166A ALA* 3.0 23.2 + - - +
179A TRP* 3.6 36.0 - - + +
182A ILE* 4.0 15.4 - - + +
183A SER* 3.2 27.0 - - - -
186A CYS* 4.8 1.1 - - - -
80B ALA* 4.0 23.1 - - + -
302D L3P 5.6 2.0 - - + -
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Residues in contact with GLY 163 (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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124A TYR* 3.3 15.1 + - - -
159A MET 3.1 11.2 + - - -
160A CYS 3.2 4.5 + - - -
161A VAL 3.2 0.2 - - - -
162A THR* 1.3 79.0 + - - +
164A LEU* 1.3 60.7 + - - +
166A ALA* 3.2 7.4 + - - +
167A ALA 3.1 17.3 + - - -
183A SER* 4.0 3.8 - - - -
229A TRP* 4.3 1.2 + - - -
301A RET 3.7 30.5 - - - -
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Residues in contact with LEU 164 (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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121A TRP* 3.7 34.5 - - + +
124A TYR* 3.2 30.1 - - + -
125A LEU* 4.3 18.2 - - + -
160A CYS 3.0 9.4 + - - +
161A VAL* 3.6 15.7 - - + +
163A GLY* 1.3 73.7 - - - +
165A ALA* 1.3 65.9 + - - +
167A ALA* 3.3 1.4 + - + +
168A LEU* 3.0 46.1 + - + +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A VAL* 2.9 19.4 + - + +
162A THR* 3.6 2.2 - - - +
163A GLY 3.3 0.2 - - - -
164A LEU* 1.3 77.3 - - - +
166A ALA* 1.3 53.6 + - - +
168A LEU* 3.4 3.6 + - - +
169A THR* 2.6 37.6 + - - -
179A TRP* 3.6 40.4 - - + -
89B LEU* 3.9 16.8 - - + +
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Residues in contact with ALA 166 (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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162A THR 3.0 8.3 + - - +
163A GLY* 3.4 11.4 - - - +
165A ALA* 1.3 75.1 - - - +
167A ALA* 1.3 64.7 + - - +
169A THR* 3.2 9.7 + - - -
176A ARG* 3.0 35.2 + - - +
179A TRP* 3.3 32.9 - - + -
180A TYR* 4.2 5.8 - - - +
229A TRP* 3.9 15.5 - - + -
301A RET 6.0 0.2 - - + -
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Residues in contact with ALA 167 (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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94A LEU* 3.7 12.2 - - - +
96A MET* 4.5 2.6 - - - +
119A THR* 4.6 13.6 - - + +
121A TRP* 5.5 0.2 - - + -
124A TYR* 3.4 37.7 - - + +
163A GLY 3.1 2.6 + - - -
164A LEU* 3.7 8.7 - - + +
166A ALA* 1.3 78.8 - - - +
168A LEU* 1.3 60.3 + - + +
176A ARG* 2.9 28.1 + - - +
229A TRP* 4.4 2.4 - - - -
234A GLU* 4.4 10.7 - - + +
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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