Contacts of the helix formed by residues 162 - 175 (chain A) in PDB entry 3N3B
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 PHE 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.6 30.0 - - + +
66A LEU* 3.5 41.5 - - + -
67A ASP* 3.3 37.0 - - - -
105A TYR* 3.9 5.2 - - - -
157A LEU* 3.0 34.1 + - + +
158A GLU* 3.6 36.1 - - + +
160A PHE 3.3 0.6 - - - -
161A LEU* 1.3 76.2 - - - +
163A TYR* 1.3 56.1 + - + +
164A SER 3.2 1.3 - - - -
165A GLY* 3.0 19.5 + - - -
166A PHE* 3.0 45.5 + + + -
188A ILE* 5.8 0.7 - - + -
192A GLU* 5.9 1.1 - - + -
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU 3.8 14.0 + - - -
159A SER* 3.7 23.1 - - - -
160A PHE 3.2 15.2 + - - +
161A LEU 3.1 2.0 - - - -
162A PHE* 1.3 74.1 - - + +
164A SER* 1.3 62.5 + - - +
165A GLY 3.1 1.6 - - - -
166A PHE* 3.7 30.9 - + + -
167A TRP* 3.2 17.5 + - - +
189A ILE* 3.6 19.8 + - + +
192A GLU* 5.3 2.8 - - - +
193A ALA 5.4 0.3 + - - -
250A VAL* 4.6 0.7 - - - +
253A PHE* 3.4 33.1 - + + +
254A LEU* 4.5 3.8 - - + -
257A ASN* 3.3 45.8 - - + +
286A LEU* 5.3 2.2 - - + -
322A PEO 4.6 2.1 + - - -
85D ASN* 3.0 35.8 + - - -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 5.0 0.5 - - - +
63A LEU* 5.9 0.7 - - - +
134A LYS* 4.6 0.5 + - - -
161A LEU 3.2 5.5 + - - -
162A PHE 4.5 0.2 - - - -
163A TYR* 1.3 78.7 - - - +
165A GLY* 1.3 55.1 + - - +
167A TRP* 4.1 1.0 - - - +
233A GLU* 2.7 28.3 + - - -
236A TYR* 4.0 15.1 - - - -
237A THR* 4.1 17.0 - - - -
240A LEU* 5.1 3.0 - - - +
241A TYR* 2.7 37.3 + - - -
250A VAL* 3.8 12.9 - - - +
254A LEU* 3.8 16.9 - - - +
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.4 32.1 - - - +
63A LEU* 4.4 11.7 - - - +
162A PHE 3.0 7.7 + - - -
164A SER* 1.3 82.1 + - - +
166A PHE* 1.3 64.3 + - - +
167A TRP 3.1 2.7 + - - -
168A LEU* 3.4 4.9 + - - +
169A PRO* 3.3 16.3 - - - +
236A TYR* 6.4 0.7 - - - -
240A LEU* 5.8 1.6 - - - -
241A TYR* 4.4 1.1 - - - -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.1 20.0 - - + -
105A TYR* 4.2 7.4 - - - -
158A GLU 5.0 3.6 - - - -
162A PHE* 3.0 45.8 + + + -
163A TYR* 3.6 44.4 + + + -
165A GLY* 1.3 73.6 - - - +
167A TRP* 1.3 64.0 + - - +
169A PRO* 3.3 13.0 - - + +
170A MET* 3.3 20.5 - - + +
185A ILE* 3.6 29.4 - - + -
188A ILE* 3.8 24.5 - - + -
189A ILE* 4.0 22.7 - - + -
192A GLU* 5.1 5.4 - - + -
253A PHE* 4.6 1.3 - - + -
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Residues in contact with TRP 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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163A TYR 3.2 18.1 + - - +
164A SER 4.1 9.2 - - - +
165A GLY 3.1 0.4 - - - -
166A PHE* 1.3 76.8 - - - +
168A LEU* 1.3 66.8 + - + +
170A MET* 3.2 6.7 + - - +
171A TYR* 2.9 58.6 + + + -
241A TYR* 3.9 9.2 - + - +
246A TRP* 3.5 49.4 - + + -
249A ASP* 3.7 31.8 + - + -
250A VAL* 3.6 23.3 - - + -
253A PHE* 3.7 36.5 - + + -
282A ILE* 3.5 28.4 - - + +
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Residues in contact with LEU 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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55A LEU* 3.8 33.9 - - + -
56A THR* 3.6 38.6 - - + +
59A VAL* 3.9 12.6 - - + -
60A PHE* 5.9 0.9 - - + -
165A GLY 3.4 7.2 + - - +
167A TRP* 1.3 84.9 - - + +
169A PRO* 1.4 68.7 - - + +
171A TYR* 3.2 3.8 + - + +
172A PHE* 3.0 59.1 + - + -
241A TYR* 3.9 14.3 + - + +
246A TRP* 4.1 11.0 - - + -
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Residues in contact with PRO 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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59A VAL* 5.3 0.2 - - + -
60A PHE* 4.4 18.8 - - + -
165A GLY 3.3 11.9 - - - +
166A PHE* 3.3 15.5 - - - +
168A LEU* 1.4 95.2 - - + +
170A MET* 1.3 62.4 + - + +
172A PHE* 3.9 10.8 - - + +
173A SER* 3.1 27.0 + - - -
178A LEU* 5.0 1.5 - - + +
181A THR* 5.0 3.8 - - + -
182A ALA* 3.5 15.2 - - - +
185A ILE* 3.8 38.6 - - + -
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Residues in contact with MET 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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166A PHE* 3.3 14.8 - - + +
167A TRP* 3.2 9.6 + - - +
168A LEU 3.2 0.8 - - - -
169A PRO* 1.3 81.6 - - - +
171A TYR* 1.3 63.3 + - - +
173A SER* 3.4 1.3 - - - -
174A SER* 3.3 17.8 + - - -
182A ALA* 3.8 23.8 - - + +
185A ILE* 4.1 18.8 - - + -
186A ARG* 4.0 17.3 - - + +
189A ILE* 4.3 10.1 - - + -
253A PHE* 5.1 2.0 - - + -
282A ILE* 4.2 16.4 - - + +
285A ALA* 3.4 39.6 - - + +
286A LEU* 3.7 29.2 - - + -
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Residues in contact with TYR 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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52A GLU* 5.2 1.3 - - - -
167A TRP* 2.9 49.9 + + + +
168A LEU* 3.2 4.9 + - + +
170A MET* 1.3 74.4 - - - +
172A PHE* 1.3 84.4 + + - +
174A SER* 2.6 29.3 + - - -
175A ARG* 3.2 34.5 + - + +
246A TRP* 3.5 46.0 + + - -
279A ASN* 5.8 3.6 - - - -
281A ALA* 6.4 0.4 - - + -
282A ILE* 3.8 12.3 - - + +
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Residues in contact with PHE 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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48A LEU* 3.7 28.9 - - + -
52A GLU* 3.8 26.0 - - + -
56A THR* 3.6 21.8 - - + -
168A LEU* 3.0 50.2 + - + +
169A PRO* 3.9 8.5 - - + +
171A TYR* 1.3 94.1 - + - +
173A SER* 1.3 58.3 + - - +
175A ARG* 3.1 5.1 + - + +
176A GLY 3.1 4.5 + - - -
177A LYS* 2.8 54.7 + - + +
178A LEU* 3.7 26.0 - - + -
246A TRP* 4.8 1.3 - + - -
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Residues in contact with SER 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 PRO 3.1 19.5 + - - -
170A MET* 3.4 8.7 - - - -
171A TYR 3.2 0.2 - - - -
172A PHE* 1.3 76.3 - - - +
174A SER* 1.3 60.3 + - - +
176A GLY* 3.2 12.7 + - - -
177A LYS 3.6 7.4 + - - +
179A THR* 4.9 10.0 - - - +
182A ALA* 3.8 13.4 - - - +
186A ARG* 3.5 26.8 + - - -
285A ALA* 4.4 6.6 - - - +
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Residues in contact with SER 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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170A MET 3.3 5.2 + - - -
171A TYR* 2.6 33.2 + - - -
173A SER* 1.3 79.6 - - - +
175A ARG* 1.3 60.8 + - - +
176A GLY 3.2 1.4 + - - -
281A ALA* 3.8 39.6 - - - +
282A ILE* 5.0 0.3 - - - +
285A ALA* 4.9 2.0 - - - +
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Residues in contact with ARG 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 TYR* 3.2 37.1 + - + +
172A PHE* 3.1 10.1 + - + +
174A SER* 1.3 81.1 + - - +
176A GLY* 1.3 62.0 + - - +
177A LYS* 3.3 39.5 + - + +
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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