Contacts of the helix formed by residues 169 - 189 (chain A) in PDB entry 2K7W
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 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR 3.4 0.4 + - - -
168A PRO* 1.3 79.5 + - - +
170A TRP* 1.3 68.6 + - - +
171A GLN* 3.0 10.1 + - + +
172A THR* 3.2 36.9 + - - +
173A VAL* 3.6 11.0 - - - +
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Residues in contact with TRP 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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69A GLU* 5.4 5.5 + - - -
166A GLY 5.6 1.6 - - - +
167A THR* 3.1 30.2 + - + +
168A PRO* 3.2 3.1 - - + -
169A THR* 1.3 80.0 - - - +
171A GLN* 1.3 85.7 + - + +
173A VAL* 3.1 16.4 + - + +
174A THR* 2.8 39.7 + - - -
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Residues in contact with GLN 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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169A THR* 3.0 3.6 - - + -
170A TRP* 1.3 106.6 - - + +
172A THR* 1.3 63.6 + - - +
174A THR* 3.1 11.7 + - - -
175A ILE* 3.1 36.6 + - + +
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A THR* 3.2 30.5 + - - +
171A GLN* 1.3 77.7 - - - +
173A VAL* 1.3 59.2 + - - +
175A ILE* 3.2 16.6 + - + +
176A PHE* 2.8 29.3 + - + +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 5.2 16.4 - - + +
168A PRO 5.3 2.0 - - - +
169A THR 3.6 15.5 - - - +
170A TRP* 3.1 15.0 + - + +
172A THR* 1.3 79.2 - - - +
174A THR* 1.3 60.0 + - - +
176A PHE* 3.2 12.0 + - + +
177A VAL* 3.0 34.9 + - + +
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.0 24.6 - - + +
73A ASN* 5.4 4.5 - - - +
170A TRP* 2.8 27.6 + - - -
171A GLN* 3.1 12.4 + - - -
173A VAL* 1.3 76.3 - - - +
175A ILE* 1.3 63.2 + - + +
177A VAL* 3.4 7.5 + - - +
178A ALA* 3.0 24.7 + - + +
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Residues in contact with ILE 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 GLN* 3.1 26.4 + - + +
172A THR* 3.2 17.7 + - + +
174A THR* 1.3 75.2 - - + +
176A PHE* 1.3 60.0 + - - +
178A ALA* 3.4 6.9 + - + +
179A GLY* 2.8 27.5 + - - -
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Residues in contact with PHE 176 (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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104A ASN* 6.3 0.2 - - - -
106A ASN* 3.4 33.7 - - + -
108A GLY* 4.0 23.8 - - - -
164A TYR* 4.2 12.6 - - - -
172A THR* 2.8 15.2 + - + +
173A VAL* 3.3 17.5 - - + +
175A ILE* 1.3 76.9 - - - +
177A VAL* 1.3 72.3 + - + +
179A GLY* 3.2 2.0 + - - -
180A VAL* 3.0 42.8 + - + +
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Residues in contact with VAL 177 (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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66A ILE* 6.5 1.3 - - + -
70A LEU* 4.3 24.5 - - + -
108A GLY* 5.3 3.4 - - - +
111A VAL* 4.4 20.0 - - + -
112A ALA* 4.0 27.4 - - + +
173A VAL* 3.0 26.0 + - + +
174A THR* 3.8 6.3 - - - +
175A ILE 3.4 0.2 - - - -
176A PHE* 1.3 83.6 - - + +
178A ALA* 1.3 63.1 + - - +
180A VAL* 3.4 6.6 + - - +
181A LEU* 3.1 32.2 + - + +
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Residues in contact with ALA 178 (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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70A LEU* 5.8 4.0 - - + +
73A ASN* 6.0 2.5 - - - +
76A LEU* 4.7 23.5 - - + +
174A THR* 3.0 18.4 + - + +
175A ILE* 3.7 8.1 - - + +
177A VAL* 1.3 76.6 - - - +
179A GLY* 1.3 54.2 + - - +
181A LEU* 3.3 4.1 + - - +
182A THR* 2.7 40.2 + - - +
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Residues in contact with GLY 179 (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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175A ILE* 2.8 20.8 + - - -
176A PHE* 3.7 1.3 - - - -
178A ALA* 1.3 73.8 - - - +
180A VAL* 1.3 56.6 + - - +
182A THR* 3.2 7.5 + - - -
183A ALA* 2.8 31.2 + - - +
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Residues in contact with VAL 180 (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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99A MET* 3.8 33.9 - - + -
106A ASN* 5.2 4.9 - - - +
108A GLY 5.7 2.2 - - - -
109A ARG* 4.9 7.0 - - + -
112A ALA* 4.6 9.2 - - + -
176A PHE* 3.0 44.9 + - + +
177A VAL* 3.7 6.7 - - - +
179A GLY* 1.3 73.9 - - - +
181A LEU* 1.3 64.3 + - - +
183A ALA* 3.3 15.5 + - - +
184A SER* 3.3 15.6 + - - +
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Residues in contact with LEU 181 (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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70A LEU* 5.6 1.3 - - + -
76A LEU* 4.4 23.3 - - + -
80A ILE* 5.9 4.9 - - + -
99A MET* 4.4 11.9 - - + -
112A ALA* 3.4 33.9 - - + +
115A TYR* 3.7 27.6 - - + -
116A PHE* 4.3 21.1 - - + -
177A VAL* 3.1 31.4 + - + +
178A ALA* 3.7 3.6 - - - +
180A VAL* 1.3 79.7 - - - +
182A THR* 1.3 62.6 + - - +
184A SER* 3.5 3.0 + - - -
185A LEU* 3.1 23.9 + - - +
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Residues in contact with THR 182 (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 LEU* 4.0 6.6 - - - +
79A MET* 3.9 28.6 - - + +
178A ALA* 2.7 26.6 + - - +
179A GLY* 3.5 8.0 - - - -
181A LEU* 1.3 77.1 - - - +
183A ALA* 1.3 52.8 + - - +
185A LEU* 3.2 7.3 + - - +
186A THR* 2.6 45.7 + - - +
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Residues in contact with ALA 183 (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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179A GLY 2.8 14.0 + - - +
180A VAL* 3.5 12.8 - - - +
181A LEU 3.3 0.2 - - - -
182A THR* 1.3 74.8 - - - +
184A SER* 1.3 63.4 + - - +
186A THR* 3.0 17.7 + - - -
187A ILE* 3.2 22.8 + - + +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.7 7.4 + - - -
95A VAL* 4.2 22.2 - - - -
98A ASP* 3.8 23.6 + - - +
99A MET* 3.4 31.9 - - - +
180A VAL 3.3 6.1 + - - -
181A LEU 4.0 5.4 - - - -
183A ALA* 1.3 77.6 - - - +
185A LEU* 1.3 58.1 + - - +
187A ILE* 3.2 4.6 + - - -
188A TRP* 3.0 28.3 + - - +
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Residues in contact with LEU 185 (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 LEU* 5.5 1.1 - - + -
79A MET* 3.7 54.1 - - + +
80A ILE* 4.7 11.4 - - + +
82A ALA 5.9 0.4 - - - +
83A VAL* 4.5 22.7 - - + -
95A VAL* 5.8 0.2 - - - +
116A PHE* 5.5 9.0 - - + -
181A LEU 3.1 18.6 + - - +
182A THR* 3.5 5.8 - - - +
184A SER* 1.3 76.9 - - - +
186A THR* 1.3 56.6 + - - +
188A TRP* 4.1 12.1 - - + -
189A LYS* 2.9 42.6 + - + +
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Residues in contact with THR 186 (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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182A THR* 2.6 31.5 + - - +
183A ALA* 3.0 11.1 + - - -
185A LEU* 1.3 77.8 - - - +
187A ILE* 1.3 64.3 + - + +
189A LYS* 4.1 14.3 - - - +
190A LYS* 4.4 4.2 + - - +
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Residues in contact with ILE 187 (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 ARG* 3.4 25.7 + - - +
98A ASP* 3.7 18.6 - - - +
183A ALA* 3.3 17.7 - - + +
184A SER* 3.2 3.7 + - - +
186A THR* 1.3 78.5 - - + +
188A TRP* 1.3 64.4 + - - +
190A LYS* 3.6 15.3 + - - +
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Residues in contact with TRP 188 (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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83A VAL* 6.2 6.1 - - + -
84A ASP* 5.2 17.9 - - + -
87A SER* 5.6 3.6 - - - -
90A GLU* 4.2 10.8 - - + -
91A VAL* 3.5 52.0 + - + +
94A ARG* 3.2 50.0 - - + +
95A VAL* 4.2 17.0 - - + -
116A PHE* 6.3 0.4 - + - -
184A SER 3.0 12.7 + - - +
185A LEU* 3.1 16.4 + - + +
187A ILE* 1.3 76.4 - - - +
189A LYS* 1.3 57.7 + - + +
190A LYS* 2.7 51.0 + - - +
192A GLY 5.5 0.4 - - - -
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Residues in contact with LYS 189 (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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82A ALA* 2.8 35.2 + - + +
83A VAL* 4.5 1.8 - - + -
84A ASP* 2.6 36.8 + - - +
185A LEU* 2.9 28.7 + - + +
186A THR* 4.1 9.6 - - - +
188A TRP* 1.3 71.5 - - + +
190A LYS* 1.3 55.8 + - - +
191A MET* 2.9 15.5 + - - -
192A GLY* 4.2 20.2 - - - +
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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
------------------------------------------------------------
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