Contacts of the helix formed by residues 158 - 175 (chain A) in PDB entry 7V3X
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A SER* 1.3 78.1 - - - +
159A VAL* 1.3 59.6 + - - +
161A ARG* 3.5 19.8 - - - +
162A ARG* 3.5 22.0 + - - +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER 3.1 4.1 - - - +
158A SER* 1.3 76.0 - - - +
160A VAL* 1.3 65.3 + - + +
161A ARG 3.2 0.2 - - - -
162A ARG* 3.4 24.0 + - - +
163A GLU* 3.3 27.9 + - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 4.1 35.1 - - + -
157A SER* 3.0 20.6 + - - +
159A VAL* 1.3 76.7 - - + +
161A ARG* 1.3 56.9 + - - +
163A GLU* 3.5 1.9 + - - +
164A LEU* 2.9 41.0 + - + +
194A TYR* 3.3 48.2 - - + -
196A VAL* 5.3 4.0 - - + -
197A GLU* 5.0 5.2 - - + -
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Residues in contact with ARG 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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157A SER 3.4 5.4 + - - +
158A SER* 3.5 14.8 - - - +
159A VAL 3.2 0.2 - - - -
160A VAL* 1.3 79.1 - - - +
162A ARG* 1.3 58.2 + - + +
164A LEU* 3.6 2.9 - - - +
165A PHE* 2.8 37.8 + - + +
195A GLY 5.7 0.2 + - - -
196A VAL* 3.5 36.0 - - + +
199A PHE* 3.6 34.9 + - - +
200A VAL* 3.8 21.5 - - + +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 3.5 29.8 + - - +
159A VAL* 3.4 23.2 + - - +
161A ARG* 1.3 78.9 - - + +
163A GLU* 1.3 59.1 + - + +
165A PHE* 3.5 13.2 - - + +
166A ARG* 2.8 35.0 + - - +
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Residues in contact with GLU 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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122A ASP* 5.6 2.7 - - - +
123A LEU* 3.2 33.6 - - + +
151A PHE* 3.5 29.8 - - + -
159A VAL* 3.3 15.8 + - + +
162A ARG* 1.3 77.5 - - + +
164A LEU* 1.3 57.5 + - - +
166A ARG* 3.5 10.3 - - - +
167A LEU* 3.0 26.7 + - - +
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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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43A LEU* 5.3 0.2 - - + -
147A VAL* 4.1 20.4 - - + -
151A PHE* 4.1 19.0 - - + -
160A VAL* 2.9 22.1 + - + +
161A ARG* 3.6 4.5 - - - +
163A GLU* 1.3 73.4 - - - +
165A PHE* 1.3 55.3 + - - +
167A LEU* 2.9 14.6 + - + +
168A VAL* 2.9 36.0 + - + +
180A MET* 3.4 33.0 - - + -
196A VAL* 5.7 1.1 - - + -
197A GLU* 3.5 47.6 - - + +
200A VAL* 4.1 11.7 - - + -
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Residues in contact with PHE 165 (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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161A ARG* 2.8 24.2 + - + +
162A ARG* 3.5 13.9 - - + +
164A LEU* 1.3 71.7 - - - +
166A ARG* 1.3 58.2 + - + +
168A VAL* 3.4 2.2 + - + +
169A ALA* 2.8 54.7 + - + +
200A VAL* 3.5 23.9 - - + +
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Residues in contact with ARG 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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123A LEU* 6.2 1.8 - - + -
127A ILE* 5.1 1.3 - - - -
162A ARG 2.8 21.5 + - - +
163A GLU* 3.5 13.5 - - - +
165A PHE* 1.3 78.5 - - + +
167A LEU* 1.3 63.3 + - - +
169A ALA* 3.4 4.0 + - - +
170A ARG* 2.9 27.8 + - - +
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Residues in contact with LEU 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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76A PHE* 5.9 1.6 - - + -
123A LEU* 6.3 3.1 - - + -
126A LEU* 4.6 13.5 - - + -
127A ILE* 3.2 29.8 - - + -
130A ILE* 4.5 7.6 - - + -
144A ILE* 4.4 14.4 - - + -
147A VAL* 3.8 31.6 - - + -
151A PHE* 5.7 3.8 - - + -
163A GLU 3.0 13.5 + - - +
164A LEU* 2.9 20.2 + - + +
166A ARG* 1.3 71.0 - - - +
168A VAL* 1.3 60.2 - - - +
170A ARG* 3.7 2.6 + - - +
171A LEU* 3.1 45.2 + - + +
180A MET* 4.6 4.3 - - - -
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Residues in contact with VAL 168 (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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41A SER* 3.7 22.2 - - - +
164A LEU* 2.9 20.0 + - + +
165A PHE* 3.8 6.1 - - + +
167A LEU* 1.3 73.7 - - - +
169A ALA* 1.3 59.6 + - - +
171A LEU* 3.0 11.8 + - - +
172A LYS* 2.9 30.9 + - + +
180A MET* 3.7 30.7 - - + -
200A VAL* 4.5 20.0 - - + +
201A SER* 4.7 4.3 - - - +
202A ASP* 4.0 17.7 - - - +
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Residues in contact with ALA 169 (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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165A PHE* 2.8 46.0 + - + +
166A ARG* 3.9 4.5 - - - +
168A VAL* 1.3 73.0 - - - +
170A ARG* 1.3 60.9 + - - +
172A LYS* 3.5 8.1 + - - +
173A GLN* 3.1 26.9 + - - +
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Residues in contact with ARG 170 (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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127A ILE* 3.7 39.3 - - + -
166A ARG 2.9 17.9 + - - +
167A LEU 3.7 0.2 - - - +
169A ALA* 1.3 76.4 - - - +
171A LEU* 1.3 49.1 + - - +
173A GLN* 3.0 18.7 + - - +
174A ILE* 2.8 39.2 + - + +
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Residues in contact with LEU 171 (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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41A SER* 5.2 4.3 - - - +
127A ILE* 5.2 2.7 - - + -
130A ILE* 4.1 27.8 - - + -
134A ILE* 4.9 2.5 - - + -
142A VAL* 4.9 2.2 - - + -
144A ILE* 4.1 17.0 - - + -
167A LEU* 3.1 40.6 + - + +
168A VAL* 3.0 11.7 + - - +
170A ARG* 1.3 78.1 - - + +
172A LYS* 1.3 56.5 + - - +
174A ILE* 3.6 9.6 + - + +
175A GLY 3.1 5.9 + - - -
176A ALA* 3.0 40.6 + - + +
178A THR* 3.8 29.6 - - + +
180A MET* 4.5 5.8 - - - -
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Residues in contact with LYS 172 (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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39A GLY 3.9 19.5 - - - +
40A ARG* 5.8 4.9 - - + +
168A VAL* 2.9 15.4 + - + +
169A ALA* 3.7 11.7 - - - +
171A LEU* 1.3 72.8 - - - +
173A GLN* 1.3 64.4 + - - +
175A GLY* 3.3 11.8 + - - -
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Residues in contact with GLN 173 (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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169A ALA 3.1 16.8 + - - +
170A ARG* 3.0 17.2 + - - +
172A LYS* 1.3 73.1 - - - +
174A ILE* 1.3 69.4 - - + +
175A GLY* 3.0 3.8 + - - -
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Residues in contact with ILE 174 (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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127A ILE* 4.8 11.9 - - + -
130A ILE* 5.9 1.1 - - + -
131A ASN* 3.4 46.7 - - + +
134A ILE* 3.4 44.0 - - + +
135A GLN* 4.3 7.8 - - - +
170A ARG* 2.8 33.0 + - + +
171A LEU* 3.7 13.7 - - + +
172A LYS 3.5 0.2 - - - -
173A GLN* 1.3 77.4 - - + +
175A GLY* 1.3 59.2 + - - +
176A ALA* 4.5 2.2 - - + +
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Residues in contact with GLY 175 (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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38A ILE* 6.1 0.5 - - - +
39A GLY* 4.4 11.5 - - - -
134A ILE* 6.4 0.2 - - - -
140A ARG* 4.8 11.3 + - - +
171A LEU 3.1 4.2 + - - -
172A LYS* 3.6 12.3 - - - -
173A GLN 3.0 5.4 - - - -
174A ILE* 1.3 79.2 - - - +
176A ALA* 1.3 59.7 + - - +
177A THR 4.2 1.0 + - - -
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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