Contacts of the helix formed by residues 162 - 171 (chain C) in PDB entry 4NH1
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 GLY 162 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LEU* 4.4 4.2 - - - +
160C GLY* 4.5 0.4 - - - -
161C THR* 1.3 83.8 + - - +
163C PHE* 1.3 58.3 + - - +
164C PRO* 3.6 2.5 - - - -
165C HIS* 3.8 8.3 - - - -
166C ILE* 3.0 27.0 + - - +
186D ARG 3.5 11.4 - - - -
187D LEU* 3.3 25.9 - - - +
188D TYR 5.3 0.4 - - - -
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Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 3.3 39.9 - - + -
89C LEU* 3.9 11.9 - - + +
94C ILE* 4.9 3.8 - - + -
97C MET* 3.5 41.1 - - + -
120C LEU* 4.1 12.1 - - + -
121C PRO* 3.3 46.4 - - + +
159C PHE* 3.5 22.6 + - + +
160C GLY* 5.1 1.1 - - - +
161C THR 3.6 1.0 - - - +
162C GLY* 1.3 74.4 - - - +
164C PRO* 1.3 80.0 - - + +
166C ILE* 3.4 2.3 - - + +
167C LEU* 3.1 41.2 + - + +
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Residues in contact with PRO 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 4.0 17.7 - - + -
121C PRO 3.5 18.4 - - - +
122C ILE* 3.9 33.7 - - + -
136C TYR* 3.5 33.0 - - + -
161C THR 4.5 0.7 - - - +
162C GLY 3.8 1.3 - - - -
163C PHE* 1.3 101.3 - - + +
165C HIS* 1.3 64.4 + - + +
167C LEU* 3.4 6.0 + - + +
168C PHE* 3.1 27.8 - - - -
175C ARG* 5.8 0.2 - - - -
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Residues in contact with HIS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 4.5 4.0 - - + -
136C TYR* 4.1 23.0 + + - -
161C THR 3.3 26.3 + - - -
162C GLY* 3.8 10.5 - - - +
163C PHE 3.2 0.6 - - - -
164C PRO* 1.3 82.9 - - + +
166C ILE* 1.3 58.8 + - - +
167C LEU 3.4 0.7 + - - -
168C PHE* 3.5 4.9 + - - +
169C MET* 3.2 26.5 + - - +
175C ARG* 5.4 4.3 + - - +
183D PHE* 3.7 23.0 - + - -
185D PRO* 3.3 31.3 - - + +
186D ARG 3.7 16.1 + - - -
187D LEU* 4.4 7.2 - - + -
192D ILE* 3.6 24.0 - - + +
197D TYR* 4.7 2.8 + - - -
200D GLN* 4.9 1.7 + - - -
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Residues in contact with ILE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 6.5 0.2 - - + -
47A ARG* 3.5 27.8 - - - +
52A GLU* 4.9 2.0 - - + -
54A PHE* 4.2 15.7 - - + -
88C ILE 5.0 0.9 - - - +
89C LEU* 3.8 22.7 - - + +
94C ILE* 4.2 13.9 - - + +
162C GLY 3.0 21.9 + - - +
163C PHE* 3.4 7.4 - - - +
165C HIS* 1.3 73.8 - - - +
167C LEU* 1.3 66.4 + - - +
168C PHE 3.4 0.2 - - - -
169C MET* 3.3 20.2 + - + +
170C VAL* 3.4 15.2 + - + +
187D LEU* 3.8 13.7 - - + -
188D TYR* 4.1 28.3 - - + +
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 3.8 28.7 - - + +
98C LEU* 4.1 26.2 - - + +
101C TYR* 6.2 0.4 - - + -
120C LEU* 3.9 18.2 - - + -
163C PHE* 3.1 48.1 + - + +
164C PRO* 3.4 7.2 - - + +
165C HIS 3.2 0.4 - - - -
166C ILE* 1.3 80.5 - - - +
168C PHE* 1.3 83.6 + - + +
169C MET 3.2 0.2 - - - -
170C VAL* 3.3 10.6 - - - +
171C HIS* 2.9 33.7 + - + +
174C TYR* 5.2 0.4 - - + -
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Residues in contact with PHE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 4.9 6.7 - + - -
120C LEU* 3.8 20.9 - - + -
136C TYR* 4.4 5.4 - + - -
138C PRO* 3.5 32.5 - - + -
164C PRO 3.1 25.7 + - - +
165C HIS 3.5 2.2 + - - +
167C LEU* 1.3 84.1 - - + +
169C MET* 1.3 62.4 + - - +
171C HIS 3.5 13.5 - - - +
172C PRO* 3.2 23.2 - - - +
174C TYR* 3.3 33.0 - - + -
175C ARG* 3.5 41.1 - - + +
200D GLN* 3.4 27.8 + - - +
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.3 23.8 - - + -
42A VAL 4.1 15.3 - - - +
43A ARG* 4.5 0.4 - - - -
44A LYS* 4.0 29.5 + - + +
54A PHE* 3.9 26.0 - - + -
165C HIS 3.2 17.4 + - - +
166C ILE* 3.3 18.8 - - + +
167C LEU 3.2 0.4 - - - -
168C PHE* 1.3 80.2 - - - +
170C VAL* 1.3 61.6 + - + +
172C PRO* 3.8 10.3 - - - +
187D LEU* 4.4 4.3 - - + -
192D ILE* 4.3 17.9 - - + -
196D ALA* 4.2 20.9 - - + -
200D GLN* 4.2 11.4 - - - +
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.8 35.2 + - + +
47A ARG* 4.5 13.9 - - - +
91C ASN* 4.5 17.7 - - - +
94C ILE* 4.0 15.7 - - + -
166C ILE* 3.4 14.3 + - + +
167C LEU 3.3 11.4 - - - +
169C MET* 1.3 78.2 - - + +
171C HIS* 1.3 93.7 + - + +
172C PRO* 3.5 6.9 - - - +
173C GLU* 4.6 0.3 - - - +
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Residues in contact with HIS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASN* 5.6 2.2 - - - -
94C ILE* 3.9 18.2 - - + +
95C ALA* 5.1 7.6 - - + -
98C LEU* 3.5 27.5 - - + +
167C LEU* 2.9 16.0 + - + +
168C PHE* 3.4 20.0 - - - -
170C VAL* 1.3 114.4 - - + +
172C PRO* 1.3 61.4 - - - +
173C GLU* 3.1 28.8 + - - +
174C TYR* 3.4 18.3 + + + +
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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