Contacts of the helix formed by residues 156 - 168 (chain A) in PDB entry 2W99
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 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 3.8 26.3 + - + +
79A PRO* 4.0 6.7 - - + +
80A LEU* 3.7 39.5 - - + +
114A LYS* 4.8 3.8 - - - -
154A ALA 5.1 0.7 - - - +
155A MET* 1.3 78.6 - - - +
157A PRO* 1.3 76.0 - - + +
158A HIS* 3.1 10.0 + - - -
159A ASP* 3.0 31.7 + - - +
160A PHE* 3.2 15.9 - - - -
200A PRO* 3.4 5.8 - - - -
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Residues in contact with PRO 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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79A PRO* 4.0 14.4 - - + -
156A THR* 1.3 89.5 - - + +
158A HIS* 1.3 55.4 + - - +
160A PHE 3.0 4.3 + - - -
161A ILE* 2.9 26.8 + - - +
186A VAL* 3.2 43.7 - - + -
195A PHE* 4.1 12.3 - - + -
200A PRO* 3.6 30.5 - - + +
203A VAL* 3.9 12.1 - - + -
204A ALA* 3.1 13.9 - - - +
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.4 39.8 + - + +
76A GLU* 4.3 15.2 - - + +
79A PRO* 3.3 36.0 - - + +
156A THR* 3.1 11.4 - - - +
157A PRO* 1.3 75.7 - - - +
159A ASP* 1.3 65.3 + - - +
161A ILE* 3.7 9.8 - - + +
162A GLU* 3.2 31.7 + - + +
183A GLN* 3.5 36.6 + - + +
186A VAL* 3.9 20.0 - - + -
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Residues in contact with ASP 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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31A MET* 4.4 12.4 - - + +
76A GLU* 4.3 10.1 - - - +
114A LYS* 5.2 5.4 + - - -
154A ALA 4.1 3.3 - - - +
155A MET* 3.2 36.7 - - + +
156A THR* 3.0 33.8 + - - +
158A HIS* 1.3 78.1 - - - +
160A PHE* 1.3 59.8 + - - +
162A GLU* 4.1 5.2 + - - +
163A HIS* 3.6 16.3 + - - +
62B ARG* 5.3 4.0 + - - -
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Residues in contact with PHE 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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28A LEU* 4.0 19.1 - - + -
31A MET* 4.0 17.5 - - + -
32A LEU* 3.9 14.4 - - + -
35A GLU* 3.4 27.1 - - - -
155A MET* 3.4 39.3 - - + -
156A THR 3.2 19.5 - - - -
157A PRO 3.0 1.6 + - - -
159A ASP* 1.3 75.8 - - - +
161A ILE* 1.3 65.9 + - - +
162A GLU 3.2 1.3 - - - -
163A HIS* 2.8 8.4 + - + +
164A PHE* 2.8 43.8 + + + -
200A PRO* 4.0 2.0 - - + -
201A SER* 3.8 27.6 - - - -
204A ALA* 3.5 17.7 - - + -
237A ILE* 5.8 0.2 - - + -
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Residues in contact with ILE 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 PRO 2.9 23.2 + - - +
158A HIS* 3.7 11.0 - - + +
160A PHE* 1.3 75.4 - - - +
162A GLU* 1.3 55.1 + - - +
164A PHE* 3.5 3.6 + - - +
165A LEU* 2.8 54.8 + - + +
179A ARG* 4.4 14.4 - - + -
182A ALA* 3.9 19.1 - - + -
183A GLN* 4.3 13.7 - - + +
186A VAL* 3.8 28.7 - - + -
204A ALA* 3.7 19.5 - - + +
208A VAL* 4.2 17.5 - - + -
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Residues in contact with GLU 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 HIS* 3.2 17.1 + - + +
159A ASP* 4.2 5.2 - - - +
160A PHE 3.2 0.6 - - - -
161A ILE* 1.3 77.7 - - - +
163A HIS* 1.3 57.8 + - - +
165A LEU* 3.1 5.5 + - - +
166A SER* 2.9 29.1 + - - -
179A ARG* 2.6 57.1 + - - +
183A GLN* 4.5 2.8 - - - +
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Residues in contact with HIS 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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24A ASN* 3.7 46.1 + - - +
27A VAL* 4.6 7.7 - - + +
28A LEU* 3.4 36.1 - - + +
31A MET* 5.1 12.4 - - + +
159A ASP 3.6 11.7 + - - +
160A PHE* 2.8 17.9 + - + +
162A GLU* 1.3 72.7 - - - +
164A PHE* 1.3 75.4 + + + +
166A SER* 2.4 30.6 + - - -
167A LYS* 3.2 25.1 + - - +
236A VAL* 4.6 0.4 - - + -
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Residues in contact with PHE 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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28A LEU* 5.4 0.9 - - + -
160A PHE* 2.8 40.9 + + + -
161A ILE* 3.7 7.6 - - - +
163A HIS* 1.3 81.1 - + - +
165A LEU* 1.3 61.2 + - - +
167A LYS* 3.2 14.7 + - + +
168A MET* 3.1 30.0 + - + +
201A SER 3.9 2.9 - - - -
204A ALA* 3.9 10.1 - - + -
205A ALA* 3.5 37.2 - - + -
208A VAL* 4.5 6.3 - - + -
232A PHE* 5.3 0.2 - - - -
233A LEU* 3.5 31.6 - - + -
236A VAL* 3.9 25.8 - - + -
237A ILE* 3.8 24.7 - - + -
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Residues in contact with LEU 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 ILE* 2.8 29.5 + - + +
162A GLU* 3.3 8.1 - - - +
163A HIS 3.0 0.2 - - - -
164A PHE* 1.3 74.5 - - - +
166A SER* 1.3 61.3 + - - +
168A MET* 3.2 27.3 + - + +
175A LYS* 3.1 58.1 + - + +
178A ILE* 3.9 22.7 - - + -
179A ARG* 3.6 42.0 - - + +
208A VAL* 4.3 11.0 - - + -
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Residues in contact with SER 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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24A ASN* 5.0 5.8 + - - -
162A GLU 2.9 10.8 + - - -
163A HIS* 2.4 36.4 + - - -
165A LEU* 1.3 76.2 - - - +
167A LYS* 1.3 63.5 + - - +
168A MET 3.1 4.9 + - - +
175A LYS* 4.2 9.2 + - - +
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Residues in contact with LYS 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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24A ASN* 3.9 24.9 - - - +
25A ASP* 6.2 1.2 - - - +
28A LEU* 4.7 3.8 - - - +
163A HIS* 3.7 35.6 + - + +
164A PHE* 3.2 11.3 + - - +
166A SER* 1.3 77.8 + - - +
168A MET* 1.3 60.4 + - - +
169A PRO* 4.0 4.0 - - - +
232A PHE* 4.3 25.8 - - + -
236A VAL* 3.5 36.3 - - + +
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Residues in contact with MET 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 PHE* 3.1 17.3 - - + +
165A LEU* 3.6 25.6 - - + +
166A SER 3.1 4.0 - - - +
167A LYS* 1.3 81.3 - - - +
169A PRO* 1.3 67.4 - - + +
170A GLU* 3.1 13.8 + - + +
175A LYS* 3.4 21.0 + - + -
178A ILE* 5.5 3.1 - - - -
208A VAL* 3.6 24.7 - - + -
212A VAL* 5.2 4.7 - - - -
225A SER* 3.7 16.6 - - - +
229A LEU* 3.6 28.7 - - + -
232A PHE* 4.6 9.6 - - + -
233A LEU* 3.6 21.5 - - + -
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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