Contacts of the helix formed by residues 162 - 175 (chain A) in PDB entry 4H1V
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 ILE 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ARG* 5.8 2.5 - - - +
123A LYS* 5.9 0.4 - - + -
124A GLY* 3.8 32.5 - - - +
125A VAL* 3.9 18.8 - - + -
160A LYS* 3.3 42.2 - - + +
161A ASP* 1.3 77.0 - - - +
163A GLU* 1.3 67.9 + - + +
164A LEU 3.1 1.1 - - - -
165A GLN* 3.2 21.7 + - + +
166A ILE* 3.3 17.7 + - + +
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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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149A GLY 4.9 0.2 - - - +
150A MET* 3.4 7.0 - - - +
151A THR* 3.1 41.6 + - - +
155A VAL* 3.7 15.9 - - + -
158A GLN* 3.3 25.6 - - - +
160A LYS* 3.1 3.6 + - + +
161A ASP 3.1 0.6 - - - -
162A ILE* 1.3 81.7 - - + +
164A LEU* 1.3 63.1 + - - +
166A ILE* 3.2 23.2 + - - +
167A ARG* 2.6 65.9 + - - +
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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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155A VAL* 3.7 33.9 - - + -
161A ASP* 3.3 37.5 + - - +
162A ILE 3.1 0.2 - - - -
163A GLU* 1.3 78.5 - - - +
165A GLN* 1.3 57.1 + - - +
167A ARG* 3.0 11.4 + - + +
168A GLU* 2.9 34.6 + - + +
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Residues in contact with GLN 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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123A LYS* 3.6 38.7 - - - +
125A VAL* 4.3 22.8 - - + +
161A ASP 4.5 0.4 + - - +
162A ILE* 3.2 18.7 + - + +
164A LEU* 1.3 75.5 - - - +
166A ILE* 1.3 60.2 + - - +
168A GLU* 3.7 21.0 - - - +
169A LEU* 3.1 25.9 + - + +
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Residues in contact with ILE 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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60A ARG* 6.5 0.2 - - - -
125A VAL* 3.8 23.1 - - + -
148A PRO* 4.2 16.2 - - + +
149A GLY 4.0 22.9 - - - +
150A MET* 4.3 1.8 - - + -
162A ILE* 3.3 20.6 + - + +
163A GLU* 3.2 35.2 + - - +
164A LEU 3.1 0.2 - - - -
165A GLN* 1.3 76.2 - - - +
167A ARG* 1.3 63.6 + - - +
169A LEU* 3.4 6.9 + - + +
170A ILE* 3.1 37.9 + - + +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MET* 3.5 30.9 - - - +
151A THR* 3.4 21.6 + - - -
153A VAL 3.5 13.1 + - - -
155A VAL* 3.6 25.9 - - + +
163A GLU* 2.6 45.5 + - + +
164A LEU* 3.0 12.5 + - + +
166A ILE* 1.3 74.4 - - - +
168A GLU* 1.3 59.5 + - - +
170A ILE* 3.4 2.4 + - - +
171A LEU* 3.0 41.4 + - + +
195A GLU* 3.1 23.4 + - - +
199A ILE* 3.9 17.9 - - + +
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Residues in contact with GLU 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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164A LEU* 2.9 24.3 + - + +
165A GLN* 3.7 26.2 - - - +
167A ARG* 1.3 77.7 - - + +
169A LEU* 1.3 57.0 + - - +
171A LEU* 3.4 11.5 + - + +
172A ARG* 2.9 30.4 + - - +
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Residues in contact with LEU 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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62A PRO* 4.1 12.6 - - + -
125A VAL* 3.6 26.7 - - + -
126A SER 4.1 0.9 - - - +
127A PRO* 3.6 26.7 - - + -
147A LEU* 5.3 0.9 - - + -
148A PRO* 3.8 30.5 - - + -
165A GLN* 3.1 18.4 + - + +
166A ILE* 3.6 6.1 - - - +
168A GLU* 1.3 76.7 - - - +
170A ILE* 1.3 63.8 + - + +
172A ARG* 3.3 9.9 + - - +
173A PHE* 3.2 49.8 + - + -
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Residues in contact with ILE 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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31A VAL* 3.9 29.4 - - + -
32A GLY 5.4 1.1 - - - +
147A LEU* 3.7 22.9 - - + -
148A PRO* 3.6 21.3 - - + +
150A MET* 3.5 37.5 - - + +
166A ILE* 3.1 19.1 + - + +
167A ARG* 3.8 3.6 - - - +
168A GLU 3.3 0.2 - - - -
169A LEU* 1.3 75.8 - - + +
171A LEU* 1.3 62.2 - - - +
173A PHE* 3.1 3.3 + - - +
174A ILE* 2.9 40.3 + - + +
199A ILE* 4.1 14.6 - - + -
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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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167A ARG* 3.0 30.7 + - + +
168A GLU* 3.7 11.0 - - + +
170A ILE* 1.3 75.3 - - - +
172A ARG* 1.3 63.8 + - - +
174A ILE* 3.8 5.5 - - + +
175A SER* 3.0 29.5 + - - -
199A ILE* 4.0 32.3 - - + +
202A GLU* 4.2 10.3 - - + -
203A VAL* 4.1 23.4 - - + +
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Residues in contact with ARG 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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19A GLY* 6.0 1.2 - - - -
21A ASP* 2.8 44.8 + - - +
127A PRO* 3.3 35.9 + - - +
168A GLU 2.9 18.1 + - - +
169A LEU* 3.4 17.3 - - - +
170A ILE 3.2 0.2 - - - -
171A LEU* 1.3 76.4 - - - +
173A PHE* 1.3 68.3 + - + +
175A SER* 3.0 18.0 + - - -
176A ASN* 4.3 2.4 + - - +
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Residues in contact with PHE 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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21A ASP* 5.5 4.5 - - - -
27A GLN* 4.5 15.9 + - - -
29A VAL* 4.3 9.6 - - + +
62A PRO* 3.9 12.6 - - + -
64A ILE* 5.8 1.3 - - + -
127A PRO* 3.7 19.3 - - + -
129A PRO* 4.1 13.7 - - + -
145A VAL* 4.0 29.2 - - + -
147A LEU* 3.7 20.9 - - + -
169A LEU* 3.2 42.2 + - + -
170A ILE 3.1 7.9 + - - +
172A ARG* 1.3 93.6 - - + +
174A ILE* 1.3 57.4 + - - +
175A SER 3.2 1.6 - - - -
176A ASN* 3.3 25.8 + - - +
179A SER* 3.9 5.2 + - - -
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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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29A VAL* 3.7 27.6 - - + -
31A VAL* 3.7 17.3 - - + -
170A ILE* 2.9 34.7 + - + +
171A LEU* 3.8 11.2 - - + +
173A PHE* 1.3 73.2 - - - +
175A SER* 1.3 58.9 + - - +
176A ASN 3.1 5.4 - - - -
179A SER* 3.8 7.2 - - - -
181A ILE* 4.0 15.9 - - + -
199A ILE* 3.6 27.1 - - + +
200A SER* 4.1 11.0 - - - +
203A VAL* 3.3 18.2 - - + +
209A ARG* 3.0 29.3 + - - -
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Residues in contact with SER 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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171A LEU 3.0 13.2 + - - -
172A ARG* 3.0 20.6 + - - -
174A ILE* 1.3 75.2 - - - +
176A ASN* 1.3 64.8 + - - +
177A PRO* 3.1 13.0 - - - +
203A VAL* 4.1 18.4 - - - -
209A ARG* 4.6 2.3 + - - +
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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