Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 3NYN
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 SER 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.8 18.6 - - - -
160A ASP 3.4 9.6 - - - -
161A TYR 2.5 21.9 + - - -
162A LEU 3.2 0.7 - - - +
163A ASP* 1.3 73.5 - - - +
165A ILE* 1.3 63.7 + - - +
166A TYR* 2.9 28.4 + - - +
167A PHE* 3.2 10.6 + - - +
168A ASN* 3.5 13.2 + - - +
38B HIS* 5.5 1.1 - - - +
39B ILE* 3.7 10.6 - - - +
172B GLN* 5.7 1.3 - - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 1.3 74.1 - - - +
166A TYR* 1.3 96.0 + - + +
168A ASN* 3.0 9.1 + - + +
169A ARG* 2.9 19.9 + - - +
527A PHE* 3.8 9.6 - - + -
39B ILE* 3.9 14.8 - - + +
165B ILE* 3.6 34.5 - - + +
168B ASN* 5.1 4.3 - - + -
169B ARG* 3.6 39.3 - - + +
172B GLN* 4.7 6.5 - - - +
527B PHE* 3.6 24.7 - - + -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.8 23.2 - - + +
69A GLU* 4.1 15.1 + - + -
70A PHE* 3.7 25.6 - + + -
73A THR* 3.2 33.8 - - + +
161A TYR* 3.7 20.6 - - + -
164A SER* 2.9 16.6 + - - +
165A ILE* 1.3 95.3 - - + +
167A PHE* 1.3 57.8 + - - +
169A ARG* 3.2 9.4 + - - +
170A PHE* 2.9 24.1 + - - +
169B ARG* 4.7 5.5 + - - -
526B VAL 5.0 0.3 + - - -
527B PHE* 3.4 48.1 - + + +
528B GLY 4.9 1.5 + - - -
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 4.0 24.2 - - + -
49A LEU* 4.7 7.0 - - + -
51A ARG* 5.4 4.9 - - - -
56A LEU* 4.2 16.2 - - + -
161A TYR* 3.5 33.3 + + + +
162A LEU* 3.4 51.8 - - + +
164A SER* 3.2 4.7 + - - +
165A ILE 3.1 0.4 - - - -
166A TYR* 1.3 77.1 - - - +
168A ASN* 1.3 55.2 + - - +
170A PHE* 2.9 36.7 + + - +
171A LEU* 2.7 57.6 + - + +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.2 20.2 - - + +
42A CYS* 5.2 0.2 - - - -
46A ARG* 3.7 27.4 + - - +
162A LEU 5.3 0.7 - - - +
164A SER 3.5 10.4 + - - +
165A ILE* 3.0 14.2 + - + +
167A PHE* 1.3 75.8 - - - +
169A ARG* 1.3 63.7 + - - +
171A LEU* 3.1 18.1 + - - +
172A GLN* 3.1 19.4 + - - +
39B ILE* 4.5 16.8 - - - +
165B ILE* 4.6 8.7 - - + -
168B ASN* 3.0 33.7 + - - +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.3 29.4 - - - -
66A LEU* 4.1 6.5 - - + -
165A ILE 2.9 11.6 + - - +
166A TYR 3.3 9.2 - - - +
167A PHE 3.1 0.2 - - - -
168A ASN* 1.3 76.1 - - - +
170A PHE* 1.3 63.0 + - - +
172A GLN* 3.0 29.6 + - - +
173A TRP* 2.8 25.2 + - + -
524A LEU 3.7 5.7 + - - -
525A ASN* 2.7 51.4 + - - +
526A VAL 3.6 3.6 + - - -
527A PHE* 3.3 25.0 - - - +
165B ILE* 3.6 32.3 - - + +
166B TYR* 4.8 6.1 + - - -
527B PHE* 4.0 17.1 - - + -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.8 18.2 - - + -
56A LEU* 3.6 31.4 - - + -
60A GLN* 4.0 17.3 - - + -
62A ILE* 4.5 5.2 - - + -
63A GLY* 3.8 32.8 - - - -
66A LEU* 3.3 21.7 - - + +
161A TYR* 4.0 10.8 - - - +
166A TYR 2.9 11.1 + - - +
167A PHE* 2.9 26.9 + + - +
169A ARG* 1.3 76.6 - - - +
171A LEU* 1.3 59.6 + - + +
173A TRP* 3.1 3.5 + - + +
174A LYS* 2.8 50.3 + - + +
512A GLN* 4.5 4.5 - - - -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 4.0 23.3 - - + -
45A LEU* 4.0 8.8 - - + +
46A ARG* 3.6 63.5 - - + +
49A LEU* 3.7 29.6 - - + -
167A PHE* 2.7 34.9 + - + +
168A ASN* 3.1 12.5 + - - +
170A PHE* 1.3 72.8 - - + +
172A GLN* 1.3 58.9 + - - +
174A LYS* 3.0 5.2 + - - +
175A TRP* 2.8 28.1 + - - +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.6 23.6 - - + +
37A PRO* 3.3 37.8 + - + +
39A ILE* 3.8 22.7 - - + +
42A CYS* 3.8 17.9 - - - -
168A ASN 3.1 10.6 + - - +
169A ARG* 3.0 43.9 + - - +
171A LEU* 1.3 76.1 - - - +
173A TRP* 1.3 66.8 + - - +
175A TRP* 3.1 12.1 + - - +
176A LEU* 3.1 15.9 + - - +
164B SER* 5.5 1.0 - - - +
165B ILE* 3.9 10.7 - - - +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 5.7 1.1 - - + -
36A PHE* 3.9 25.6 - + - -
62A ILE* 4.2 21.1 - - + -
66A LEU* 4.3 5.2 - - + -
169A ARG* 2.8 30.9 + - + -
170A PHE* 3.1 11.6 + - + +
172A GLN* 1.3 75.0 - - - +
174A LYS* 1.3 61.2 + - - +
176A LEU* 3.3 29.5 + - + +
177A GLU 3.4 7.8 + - - -
511A TRP* 3.7 25.2 - + + -
515A MET* 4.1 28.0 - - + -
520A CYS* 4.0 8.1 - - + -
521A PHE* 3.6 52.4 - + - -
524A LEU* 4.3 10.1 - - + -
525A ASN* 3.0 30.2 + - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.1 17.0 - - + -
49A LEU* 4.2 19.3 - - + -
60A GLN* 2.8 29.7 + - - +
170A PHE* 2.8 35.2 + - + +
171A LEU* 3.3 12.1 - - - +
173A TRP* 1.3 75.5 - - - +
175A TRP* 1.3 67.3 + - - +
177A GLU* 2.6 53.4 + - - +
178A ARG* 3.0 32.8 + - + +
508A PRO* 4.0 9.1 - - - +
512A GLN* 3.7 2.2 - - - +
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Residues in contact with TRP 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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35A GLN 4.5 5.4 - - - -
37A PRO* 3.5 38.8 - - + -
41A GLN* 3.4 52.3 + - - +
42A CYS* 4.4 3.1 - - - -
45A LEU* 3.6 19.6 - - + +
171A LEU 2.8 16.9 + - - +
172A GLN* 3.4 8.5 - - - +
174A LYS* 1.3 70.9 - - - +
176A LEU* 1.3 91.4 + - + +
178A ARG* 3.0 14.8 + - + +
179A GLN* 3.2 58.3 + - + +
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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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33A MET 4.7 4.9 - - - +
34A LEU* 3.9 37.9 - - + +
35A GLN 3.7 21.8 - - - +
36A PHE* 3.9 23.6 - - + -
37A PRO* 5.0 0.4 - - + -
172A GLN 3.1 10.9 + - - +
173A TRP* 3.4 26.7 - - + +
174A LYS 3.2 0.2 - - - -
175A TRP* 1.3 97.8 - - + +
177A GLU* 1.3 62.4 + - - +
179A GLN* 3.0 23.7 + - + +
511A TRP* 3.9 12.8 + - + -
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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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173A TRP 3.4 2.6 + - - -
174A LYS* 2.6 62.0 + - - +
176A LEU* 1.3 75.1 - - - +
178A ARG* 1.3 66.0 + - + +
179A GLN 3.5 1.2 + - - +
506A SER* 2.7 33.3 + - - +
508A PRO* 3.3 29.6 - - - +
511A TRP* 3.3 37.6 - - + -
512A GLN* 3.1 31.6 + - - +
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Residues in contact with ARG 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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45A LEU* 3.2 34.0 - - + +
48A SER* 4.8 9.3 + - - -
49A LEU* 3.7 25.5 - - - +
174A LYS* 3.0 30.6 + - + +
175A TRP* 3.0 11.2 + - + +
177A GLU* 1.3 79.8 + - + +
179A GLN* 1.3 72.8 + - - +
180A PRO* 3.5 3.6 - - - +
508A PRO* 6.3 0.2 - - - +
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Residues in contact with GLN 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 TRP* 3.2 72.3 + - + +
176A LEU* 3.0 18.3 + - + +
177A GLU 3.8 7.1 - - - +
178A ARG* 1.3 85.0 + - - +
180A PRO* 1.3 78.9 - - + +
181A VAL* 3.6 9.7 + - - +
505A GLY* 5.8 0.7 - - - -
506A SER* 4.3 0.7 + - - -
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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