Contacts of the helix formed by residues 164 - 181 (chain A) in PDB entry 4ND1
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 ALA 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.7 13.0 - - + -
143A ASP* 5.4 0.7 - - - +
162A GLY 3.4 4.5 + - - +
163A MET* 1.3 84.5 - - - +
165A GLY* 1.3 63.7 + - - +
166A VAL 3.2 2.8 - - - +
167A LEU* 3.0 7.6 + - - +
168A ASP* 2.9 32.6 + - - +
195A HIS* 3.7 35.4 + - + +
257A MET* 5.0 0.2 - - - -
270A PRO 5.0 0.4 + - - -
271A CYS* 4.9 1.0 - - - +
272A SER* 5.2 2.9 - - - +
401A NAD 4.2 5.4 - - - -
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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
----------------------------------------------------------
164A ALA* 1.3 78.3 - - - +
166A VAL* 1.3 52.5 + - - +
168A ASP* 4.4 6.1 - - - -
169A SER* 2.7 39.3 + - - -
191A VAL* 4.4 10.1 - - - -
270A PRO* 3.2 30.8 + - - -
271A CYS* 4.3 3.4 - - - +
288A GLY* 5.9 4.4 - - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 5.0 3.6 - - + -
164A ALA 3.2 1.2 + - - +
165A GLY* 1.3 75.6 - - - +
167A LEU* 1.3 55.5 + - - +
169A SER* 4.4 1.2 - - - -
170A SER* 2.5 44.3 + - - +
253A ALA* 3.5 33.7 - - + +
256A LYS* 4.9 9.0 - - + -
257A MET* 4.3 11.9 - - + -
269A VAL* 3.6 31.4 - - + -
270A PRO* 3.1 15.7 + - + +
72B MET* 4.4 7.2 - - + -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 4.0 12.1 - - + -
164A ALA 3.0 9.8 + - - +
166A VAL* 1.3 76.1 - - - +
168A ASP* 1.3 66.2 + - - +
170A SER* 3.4 1.2 + - - -
171A ARG* 3.0 56.8 + - + +
195A HIS* 4.5 1.1 - - + -
249A ALA* 3.6 30.7 - - + -
250A PRO* 3.8 15.5 - - + -
253A ALA* 4.2 2.0 - - + +
401A NAD 3.3 33.7 - - + +
402A OXM 3.7 17.9 - - - +
68B HIS* 4.8 0.2 - - + -
72B MET* 3.9 11.4 - - + -
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Residues in contact with ASP 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 ALA* 2.9 17.7 + - - +
165A GLY* 4.0 4.0 + - - +
167A LEU* 1.3 76.1 - - - +
169A SER* 1.3 58.0 + - - +
171A ARG* 3.4 18.7 + - - +
172A PHE* 2.9 26.7 + - - +
191A VAL* 3.5 27.0 - - + +
194A GLY 5.5 0.2 - - - -
195A HIS* 2.7 45.5 + - - -
199A MET* 3.4 26.8 - - - +
232A THR* 3.6 4.9 - - - +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 2.7 28.8 + - - -
166A VAL* 4.4 1.3 - - - -
168A ASP* 1.3 70.7 - - - +
170A SER* 1.3 55.5 + - - +
172A PHE* 3.4 2.3 - - - +
173A ARG* 2.7 44.7 + - - +
189A ALA 3.5 17.7 - - - -
190A ASN* 3.7 1.3 - - - -
191A VAL* 2.9 31.2 + - - -
270A PRO* 3.7 17.2 - - - +
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Residues in contact with SER 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 VAL* 2.5 26.9 + - - +
167A LEU 3.7 1.8 - - - -
168A ASP 3.3 0.2 - - - -
169A SER* 1.3 77.5 - - - +
171A ARG* 1.3 55.3 + - - +
173A ARG* 3.7 8.8 + - - +
174A THR* 2.7 39.2 + - - -
68B HIS 3.7 5.4 - - - -
71B VAL* 3.6 20.3 - - - +
72B MET* 3.3 35.6 - - - +
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Residues in contact with ARG 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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109A ARG* 4.7 1.6 - - - +
167A LEU* 3.0 42.0 + - - +
168A ASP* 3.5 17.6 + - - +
170A SER* 1.3 73.7 - - - +
172A PHE* 1.3 64.7 + - - +
174A THR* 3.2 5.5 + - - -
175A PHE* 3.0 44.6 + - + -
199A MET* 6.1 0.2 - - - +
232A THR* 4.7 7.0 + - + -
235A ALA* 3.7 19.5 - - + +
236A TRP* 4.1 15.3 - - - +
239A VAL* 4.6 3.4 - - - +
246A ALA* 3.5 19.6 - - - +
402A OXM 2.8 42.4 + - - -
65B ASP* 5.4 0.4 + - - -
68B HIS* 3.5 41.5 + - + +
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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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168A ASP 2.9 14.6 + - - +
169A SER 3.2 7.4 + - - +
171A ARG* 1.3 77.9 - - - +
173A ARG* 1.3 61.3 + - - +
175A PHE* 3.5 2.2 + - - +
176A ILE* 3.2 36.8 + - + +
189A ALA* 3.6 13.2 - - + -
190A ASN 3.5 27.1 - - - -
191A VAL* 3.7 8.5 - - + -
201A PRO* 3.5 34.8 - - + -
202A ALA 3.9 0.4 - - - -
203A THR* 4.1 11.9 - - + -
206A VAL* 3.6 31.4 - - + -
212A LEU* 5.9 0.4 - - + -
225A ILE* 5.6 0.7 - - + -
228A ILE* 3.9 15.5 - - + -
229A VAL* 4.3 8.5 - - + -
232A THR* 3.4 21.9 + - - +
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Residues in contact with ARG 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 SER* 2.7 28.9 + - - +
170A SER* 3.7 10.2 + - - +
172A PHE* 1.3 73.0 - - - +
174A THR* 1.3 57.4 + - - +
176A ILE* 3.4 4.2 + - - +
177A ALA* 2.8 30.2 + - - +
184A ALA* 3.4 15.2 + - - +
185A SER* 3.1 31.7 + - - +
187A VAL* 2.7 36.3 + - + +
188A SER* 5.3 0.9 - - - -
189A ALA* 3.7 27.6 - - + +
71B VAL* 3.8 23.1 + - + +
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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
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170A SER 2.7 25.4 + - - -
171A ARG* 3.2 7.2 + - - -
173A ARG* 1.3 77.0 - - - +
175A PHE* 1.3 57.1 + - + +
177A ALA* 3.2 7.0 + - + +
178A GLN* 2.8 57.3 + - + +
184A ALA* 4.3 5.4 - - + +
67B THR* 3.9 29.7 + - + +
68B HIS* 4.4 8.5 - - + -
71B VAL* 3.9 16.6 + - - +
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Residues in contact with PHE 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 ARG* 3.0 30.2 + - + +
172A PHE 4.0 0.2 - - - +
174A THR* 1.3 72.8 - - + +
176A ILE* 1.3 65.0 + - - +
178A GLN* 3.5 21.8 + - - +
179A HIS* 3.2 21.7 + - - +
228A ILE* 3.8 25.6 - - + +
231A HIS* 3.3 56.8 - + + +
232A THR* 3.7 30.7 - - - -
235A ALA* 4.4 6.3 - - + -
238A GLU* 4.8 1.3 - - - -
64B LEU* 6.1 3.8 - - + -
68B HIS* 3.7 30.3 - + - -
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Residues in contact with ILE 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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172A PHE* 3.2 33.5 + - + +
173A ARG 3.6 5.2 - - - +
175A PHE* 1.3 76.0 - - - +
177A ALA* 1.3 63.3 + - - +
179A HIS* 3.2 11.1 + - - +
180A PHE* 3.2 40.0 + - + -
187A VAL* 3.9 15.9 - - + -
189A ALA* 3.8 18.8 - - + -
206A VAL* 3.8 26.7 - - + -
208A VAL* 4.2 7.9 - - + -
212A LEU* 4.9 6.3 - - + -
220A ILE* 5.8 0.7 - - + -
228A ILE* 4.0 25.1 - - + -
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Residues in contact with ALA 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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173A ARG 2.8 17.7 + - - +
174A THR* 3.5 5.4 - - + +
176A ILE* 1.3 78.0 - - - +
178A GLN* 1.3 57.7 + - + +
180A PHE 3.5 0.2 + - - -
181A GLY* 2.8 26.2 + - - -
182A VAL* 3.1 37.9 + - - +
184A ALA* 3.5 26.2 - - + -
187A VAL* 4.0 5.4 - - + -
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Residues in contact with GLN 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 THR* 2.8 32.2 + - + +
175A PHE* 3.5 28.5 - - - +
176A ILE 3.3 0.2 - - - -
177A ALA* 1.3 71.6 - - + +
179A HIS* 1.3 65.4 + - - +
181A GLY* 3.9 7.2 + - - +
64B LEU* 6.0 3.4 - - - +
67B THR* 3.7 24.4 - - - +
77B LYS* 5.7 7.0 - - - +
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Residues in contact with HIS 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 PHE 3.2 12.3 + - - +
176A ILE 3.2 8.5 + - - +
178A GLN* 1.3 80.6 - - - +
180A PHE* 1.3 77.6 + + - +
181A GLY* 3.4 0.5 + - - -
219A LEU 2.8 24.8 + - - -
220A ILE* 3.4 27.1 - - + +
224A GLN* 3.5 38.7 + - - +
228A ILE* 4.3 11.6 - - + +
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Residues in contact with PHE 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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176A ILE* 3.2 41.8 + - + +
179A HIS* 1.3 95.2 - + - +
181A GLY* 1.3 62.4 + - - +
182A VAL* 3.9 23.9 - - + +
208A VAL* 4.1 15.7 - - + -
212A LEU* 4.1 8.1 - - + -
215A PHE* 3.5 48.7 - + + -
219A LEU* 4.0 16.2 - - + -
220A ILE* 3.8 26.5 - - + -
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Residues in contact with GLY 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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177A ALA 2.8 11.4 + - - -
178A GLN* 3.9 6.4 + - - -
179A HIS 3.3 4.6 + - - -
180A PHE* 1.3 80.0 - - - +
182A VAL* 1.3 57.1 + - - +
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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