Contacts of the helix formed by residues 172 - 188 (chain A) in PDB entry 2NP5
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 PRO 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PRO 4.2 3.1 - - - +
169A ALA 4.0 9.6 - - - +
170A LEU 3.2 11.0 - - - +
171A TYR* 1.3 93.6 - - - +
173A PRO* 1.3 78.7 - - + +
174A GLU* 3.2 26.2 - - + +
175A TYR* 3.0 24.5 + - + -
176A LEU* 3.3 7.8 + - - +
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Residues in contact with PRO 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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94A PRO 5.5 0.2 - - - -
95A LEU* 3.3 47.8 - - + +
171A TYR 4.6 0.4 - - - +
172A PRO* 1.3 88.6 - - + +
174A GLU* 1.3 63.3 + - - +
176A LEU* 3.2 3.2 + - + +
177A GLU* 2.9 41.1 + - - +
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Residues in contact with GLU 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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172A PRO* 3.7 22.9 - - + +
173A PRO* 1.3 88.8 - - - +
175A TYR* 1.3 68.2 + - + +
177A GLU* 4.2 8.6 - - - +
178A HIS* 3.1 23.7 + - - +
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Residues in contact with TYR 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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160A LEU* 4.5 13.8 - - + +
170A LEU 4.8 4.9 - - - +
171A TYR* 3.8 38.4 - + - -
172A PRO* 3.0 26.0 + - + +
174A GLU* 1.3 82.8 - - + +
176A LEU* 1.3 61.9 + - + +
178A HIS* 3.4 12.0 + - - +
179A ALA* 3.0 35.0 + - + +
131C ARG* 5.5 1.7 + - - -
148C THR* 6.0 3.5 - - + +
151C ALA* 3.5 26.9 - - - +
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Residues in contact with LEU 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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93A LEU* 4.0 12.5 - - + +
94A PRO* 3.6 36.8 - - + +
95A LEU* 3.7 18.2 - - + -
160A LEU* 3.9 35.9 - - + +
164A ALA* 4.7 0.9 - - + -
171A TYR* 3.5 49.4 - - + +
172A PRO 3.8 6.3 - - - +
173A PRO* 3.2 7.3 + - + +
175A TYR* 1.3 79.8 - - + +
177A GLU* 1.3 59.5 + - - +
179A ALA* 3.5 4.1 + - - +
180A LEU* 3.0 29.8 + - - +
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Residues in contact with GLU 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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86A PHE* 3.4 37.1 - - + -
90A SER* 4.9 0.6 + - - +
93A LEU* 5.2 1.1 - - + -
95A LEU* 3.7 29.4 - - + +
173A PRO* 2.9 28.4 + - - +
174A GLU* 4.2 7.6 - - - +
175A TYR 3.3 0.2 - - - -
176A LEU* 1.3 76.3 - - - +
178A HIS* 1.3 56.9 + - - +
180A LEU* 3.4 2.1 + - - -
181A ASP* 2.9 30.2 + - - +
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Residues in contact with HIS 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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174A GLU 3.1 20.0 + - - +
175A TYR* 3.6 13.0 + - + +
177A GLU* 1.3 74.4 - - - +
179A ALA* 1.3 67.0 + - - +
181A ASP* 3.2 12.3 + - - +
182A ILE* 3.0 52.6 + - + +
145C GLU* 4.3 10.0 + - - -
148C THR* 3.9 25.2 + - + +
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Residues in contact with ALA 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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160A LEU* 3.9 25.1 - - + -
175A TYR* 3.0 28.3 + - + +
176A LEU* 3.7 5.6 - - - +
178A HIS* 1.3 79.6 + - - +
180A LEU* 1.3 63.7 + - - +
182A ILE* 3.2 8.6 + - - +
183A GLN 3.0 18.7 + - - -
148C THR* 4.9 4.5 - - + -
151C ALA* 6.5 0.7 - - + -
152C LEU* 3.6 24.4 - - + +
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Residues in contact with LEU 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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86A PHE* 3.6 24.7 - - + +
89A MSE 3.7 33.7 - - + -
90A SER* 3.7 20.2 - - - +
93A LEU* 3.8 16.2 - - + -
153A LEU* 3.8 16.8 - - + -
156A THR* 5.3 2.5 - - + -
157A VAL* 3.9 10.3 - - + -
160A LEU* 4.5 6.0 - - + +
176A LEU 3.0 18.6 + - - +
177A GLU* 3.7 3.8 - - - +
178A HIS 3.3 0.2 - - - -
179A ALA* 1.3 74.9 - - - +
181A ASP* 1.3 57.6 + - - +
183A GLN* 3.2 6.1 + - + +
184A ILE* 2.9 49.5 + - + +
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Residues in contact with ASP 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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86A PHE* 4.4 17.1 - - + +
177A GLU 2.9 18.5 + - - +
178A HIS* 3.5 13.6 - - - +
180A LEU* 1.3 74.3 - - - +
182A ILE* 1.3 61.6 + - + +
184A ILE* 3.3 7.7 + - - +
185A GLY* 2.9 26.2 + - - -
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Residues in contact with ILE 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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178A HIS* 3.0 31.3 + - + +
179A ALA 3.2 7.6 + - - +
181A ASP* 1.3 80.2 - - + +
183A GLN* 1.3 62.0 + - - +
185A GLY* 3.3 3.1 + - - -
186A MSE 3.1 30.9 + - + +
145C GLU* 3.3 28.9 - - + +
148C THR* 3.8 21.1 - - + -
149C ARG* 4.7 12.1 - - + +
152C LEU* 3.4 20.0 - - + -
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Residues in contact with GLN 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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152A LEU 3.8 13.7 + - - -
153A LEU* 3.9 17.5 - - + -
156A THR* 2.8 33.1 + - + +
179A ALA 3.0 13.7 + - - +
180A LEU* 3.7 7.6 - - - +
182A ILE* 1.3 75.1 - - - +
184A ILE* 1.3 60.7 + - - +
186A MSE 3.2 28.6 + - - +
187A ILE* 2.9 44.7 + - + +
152C LEU* 3.7 13.4 - - + +
156C THR* 3.9 2.0 + - - -
183C GLN* 3.0 31.3 + - - -
186C MSE 5.1 0.3 - - - +
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Residues in contact with ILE 184 (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* 4.2 16.8 - - + +
85A LEU* 3.8 13.0 - - + +
86A PHE* 3.5 43.5 - - + +
153A LEU* 3.9 22.9 - - + -
180A LEU* 2.9 38.8 + - + +
181A ASP* 3.8 7.4 - - - +
183A GLN* 1.3 71.6 - - - +
185A GLY* 1.3 63.9 + - - +
187A ILE* 3.1 8.0 + - + +
188A LEU* 3.0 44.5 + - + +
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Residues in contact with GLY 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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181A ASP 2.9 15.9 + - - -
182A ILE* 3.6 4.3 - - - -
183A GLN 3.3 0.2 - - - -
184A ILE* 1.3 77.6 - - - +
186A MSE 1.3 59.7 + - - +
188A LEU* 3.5 7.0 + - - +
189A GLN* 3.1 30.5 + - - +
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Residues in contact with MSE 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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149A ARG* 3.6 2.4 + - - -
182A ILE* 3.1 17.4 + - + +
183A GLN* 3.2 33.4 + - - +
185A GLY* 1.3 71.6 - - - +
187A ILE* 1.3 66.2 + - - +
189A GLN* 3.2 24.2 + - + +
149C ARG* 3.9 29.6 - - + +
152C LEU* 3.6 31.4 - - + -
183C GLN* 4.0 7.0 - - - +
186C MSE 3.6 55.6 - - + +
187C ILE* 3.9 14.6 - - + -
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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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85A LEU* 5.3 1.8 - - + -
138A LEU* 3.8 37.2 - - + -
143A THR* 3.2 10.2 - - - +
149A ARG* 2.7 57.0 + - + +
152A LEU* 4.5 1.1 - - + -
153A LEU* 4.5 15.5 - - + +
183A GLN* 2.9 46.4 + - + +
184A ILE* 3.1 10.3 + - - +
186A MSE 1.3 77.0 - - - +
188A LEU* 1.3 56.7 + - + +
186C MSE 3.9 23.1 - - + -
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Residues in contact with LEU 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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81A PRO* 5.0 0.7 - - + -
82A ALA* 3.7 36.1 - - + +
85A LEU* 4.1 7.6 - - + -
138A LEU* 3.8 20.4 - - + -
141A ILE* 3.5 31.6 - - + -
184A ILE* 3.0 29.3 + - + +
185A GLY* 3.9 6.5 - - - +
186A MSE 3.2 0.2 - - - -
187A ILE* 1.3 75.1 - - + +
189A GLN* 1.3 65.3 + - - +
190A GLY 3.2 0.7 + - - -
191A ALA* 3.0 24.0 + - + +
193A VAL* 4.2 25.4 - - + +
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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