Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 6M04
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 TYR 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A HIS* 6.2 0.3 - - - -
160A TRP* 3.0 42.9 + + + +
161A TYR* 5.2 0.9 - - - -
163A LYS* 1.3 110.7 - - + +
165A PHE* 1.3 64.3 + - - +
166A PRO* 3.7 1.8 - - - -
167A TYR* 4.1 8.4 + + + +
168A LEU* 3.5 21.3 + - - +
360B TYR* 3.5 29.6 - - - +
361B MET* 3.6 32.3 + - + +
364B LYS* 3.6 34.7 - - + +
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 6.5 0.2 - - - -
42A ALA* 5.1 9.4 - - + -
160A TRP* 6.5 0.4 - - - -
161A TYR* 3.7 21.7 + - + +
163A LYS 3.5 0.6 - - - -
164A TYR* 1.3 76.9 - - - +
166A PRO* 1.4 77.9 - - + +
167A TYR 3.2 0.2 + - - -
168A LEU* 3.3 8.0 + - + +
169A ALA* 2.9 37.3 + - + +
326A THR* 4.9 8.7 - - + -
329A PHE* 4.6 13.7 - + + -
362A LEU* 4.9 20.9 - - + -
365A LEU* 5.5 4.3 - - + -
366A LEU* 3.6 40.2 - - + -
369A TYR* 3.9 33.7 - + + -
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.2 6.1 - - - +
42A ALA* 3.7 38.4 - - + +
43A GLY* 3.8 16.4 - - - +
46A GLN* 4.2 18.2 - - + -
163A LYS* 4.6 8.3 - - - +
164A TYR 4.0 1.1 - - - -
165A PHE* 1.4 98.8 - - + +
167A TYR* 1.3 64.4 + - + +
169A ALA* 3.3 9.1 + - + +
170A LEU* 2.9 27.7 + - - +
362A LEU* 5.3 9.2 - - + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 5.2 4.0 - + - -
43A GLY* 4.7 17.5 + - - -
46A GLN* 2.4 36.4 + - - -
47A LEU* 5.0 10.2 - - - +
163A LYS 4.7 9.6 - - - -
164A TYR* 4.1 6.5 + + + +
165A PHE 3.2 0.6 - - - -
166A PRO* 1.3 81.9 - - + +
168A LEU* 1.3 61.1 + - - +
170A LEU* 3.2 14.3 + - + +
171A ILE* 3.0 33.6 + - + +
41B PHE* 3.4 46.7 - + + -
45B MET* 5.0 8.7 - - + +
49B LYS* 5.4 4.2 + - - -
361B MET* 3.6 34.3 - - + -
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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
----------------------------------------------------------
160A TRP* 5.9 8.3 - - + -
164A TYR* 3.5 18.8 + - + +
165A PHE* 3.3 8.4 + - + +
167A TYR* 1.3 77.6 - - - +
169A ALA* 1.3 60.7 + - - +
171A ILE* 3.4 16.1 + - + -
172A HIS* 2.9 33.5 + - + +
321A PHE* 6.4 1.8 - - + -
322A ILE* 5.3 10.5 - - + -
325A TYR* 6.5 1.6 - - + -
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Residues in contact with ALA 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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35A MET* 4.7 0.3 - - - +
39A ALA* 4.0 16.4 - - + -
165A PHE* 2.9 28.6 + - + +
166A PRO* 3.5 11.9 - - + +
167A TYR 3.2 0.2 - - - -
168A LEU* 1.3 76.3 - - - +
170A LEU* 1.3 56.1 + - - +
172A HIS* 3.4 3.6 + - - +
173A THR* 2.6 38.5 + - - -
369A TYR* 4.4 24.0 + - + +
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Residues in contact with LEU 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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2A PHE* 5.4 8.3 - - + -
3A THR* 4.4 15.3 - - + +
36A LEU* 5.8 4.2 - - + +
39A ALA* 4.3 8.0 - - + +
40A ILE* 3.7 28.9 - - + -
166A PRO 2.9 13.8 + - - +
167A TYR* 3.2 15.7 + - + +
169A ALA* 1.3 75.9 - - - +
171A ILE* 1.3 71.7 + - + +
173A THR* 3.3 6.5 + - - -
174A ILE* 3.0 32.9 + - + +
37B MET* 4.1 35.0 - - + -
41B PHE* 5.5 11.7 - - + -
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Residues in contact with ILE 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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167A TYR* 3.0 16.1 + - + +
168A LEU* 3.7 19.1 - - + +
169A ALA 3.3 0.2 - - - -
170A LEU* 1.3 86.9 - - + +
172A HIS* 1.3 63.8 + - - +
174A ILE* 3.3 5.8 + - + +
175A ILE* 3.0 37.6 + - + +
34B VAL* 6.1 2.0 - - + -
37B MET* 4.6 13.0 - - + -
38B VAL* 5.4 11.2 - - + -
368B SER* 5.9 2.9 - - - +
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Residues in contact with HIS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 4.7 10.1 - - + -
168A LEU* 2.9 22.3 + - + +
169A ALA* 3.9 6.3 - - - +
171A ILE* 1.3 78.2 - - - +
173A THR* 1.3 59.7 + - - +
175A ILE* 3.4 9.3 + - + +
176A LEU* 2.9 38.6 + - + +
318A LYS* 3.5 43.8 + - + +
319A PHE* 4.8 1.2 + - - -
321A PHE* 5.7 1.7 - + - -
322A ILE* 3.4 45.7 - - + +
369A TYR* 4.0 8.5 - - - +
373A ILE* 5.5 0.8 - - + +
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Residues in contact with THR 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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32A ALA* 3.9 10.8 - - + +
35A MET* 2.7 41.8 - - + -
36A LEU* 3.6 40.2 - - + -
39A ALA* 4.5 3.5 - - - +
169A ALA 2.6 23.2 + - - -
170A LEU* 3.3 6.4 + - - -
172A HIS* 1.3 74.8 - - - +
174A ILE* 1.3 59.6 + - - +
176A LEU* 3.3 2.4 + - - +
177A MET* 3.0 30.7 + - + +
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Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 6.2 0.9 - - + -
8A ALA* 4.6 15.3 - - + +
11A ASN* 4.9 12.8 - - - +
36A LEU* 4.4 19.5 - - + -
170A LEU* 3.0 21.3 + - + +
171A ILE* 3.7 5.8 - - - +
173A THR* 1.3 76.0 - - - +
175A ILE* 1.3 66.8 + - + +
177A MET* 3.4 5.8 + - + +
178A VAL* 3.0 28.7 + - + +
30B TYR* 3.4 21.3 - - + +
34B VAL* 4.9 6.7 - - + -
37B MET* 3.9 38.8 - - + -
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Residues in contact with ILE 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 ILE* 3.0 28.0 + - + +
172A HIS* 3.8 10.3 - - - +
174A ILE* 1.3 82.0 - - + +
176A LEU* 1.3 57.5 + - - +
178A VAL* 5.2 1.8 - - + -
179A SER* 2.8 39.2 + - - +
318A LYS* 5.7 8.5 - - + -
30B TYR* 5.4 5.8 - - + +
34B VAL* 6.3 4.0 - - + -
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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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32A ALA* 4.7 11.9 - - + -
35A MET* 3.8 25.1 - - + -
172A HIS* 2.9 31.1 + - - +
173A THR 3.5 6.3 - - - +
174A ILE 3.2 0.2 - - - -
175A ILE* 1.3 76.8 - - - +
177A MET* 1.3 58.6 + - - +
179A SER* 2.8 16.4 + - - -
180A SER* 2.9 16.5 + - - -
315A LYS* 4.2 24.2 - - + +
318A LYS* 5.4 3.1 - - + -
319A PHE* 6.0 1.1 - - + +
373A ILE* 5.1 3.4 - - + -
376A TYR* 3.5 50.3 - - + +
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Residues in contact with MET 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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8A ALA 4.5 11.9 - - - +
9A SER* 4.7 12.8 - - - +
12A ASP* 3.3 41.9 - - + +
13A ILE* 6.2 0.7 - - + -
29A ASP* 3.7 26.2 - - - +
32A ALA* 5.1 15.9 - - + -
33A VAL* 5.1 12.6 - - + -
36A LEU* 5.6 9.0 - - + -
173A THR* 3.0 17.7 + - + +
174A ILE* 4.2 6.1 - - + +
176A LEU* 1.3 78.0 - - - +
178A VAL* 1.3 61.1 + - + +
180A SER* 2.3 35.3 + - - +
181A ASN* 3.1 8.7 + - - +
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Residues in contact with VAL 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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11A ASN* 5.4 1.8 - - - +
12A ASP* 4.0 28.7 - - + +
174A ILE* 3.0 14.6 + - + +
175A ILE* 4.6 2.0 - - + +
177A MET* 1.3 77.7 - - + +
179A SER* 1.3 59.5 - - - +
181A ASN 4.3 0.9 - - - +
182A PHE* 2.9 39.5 + - + +
30B TYR* 3.2 56.1 - - + +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 2.8 29.8 + - - +
176A LEU* 2.8 17.3 + - - +
178A VAL* 1.3 75.7 - - - +
180A SER* 1.3 51.5 + - - +
181A ASN 3.4 0.2 - - - -
182A PHE* 3.8 16.6 - - - -
311A GLN* 2.5 38.4 + - - +
314A ILE* 4.9 10.8 - - - -
315A LYS* 3.8 21.5 - - - +
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Residues in contact with SER 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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25A ASP* 5.0 8.6 - - - +
28A MET* 5.9 7.9 - - - -
29A ASP* 6.1 1.4 - - - -
176A LEU 2.9 14.1 + - - -
177A MET* 2.3 33.1 + - - +
179A SER* 1.3 78.6 - - - +
181A ASN* 1.3 76.5 + - - +
182A PHE 3.8 0.4 - - - -
183A TRP* 4.7 6.8 - - - +
308A TYR* 6.2 0.3 - - - -
311A GLN* 3.3 19.6 + - - +
315A LYS* 4.7 8.7 - - - -
376A TYR* 5.1 5.6 - - - -
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Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 3.8 32.6 + - - +
13A ILE* 5.8 1.0 - - - +
14A GLN* 4.2 17.7 + - - +
25A ASP* 4.6 12.6 + - - +
29A ASP* 5.2 9.7 + - - -
177A MET* 3.1 10.0 + - - +
178A VAL* 3.6 2.9 - - - -
179A SER 3.4 0.2 - - - -
180A SER* 1.3 97.8 + - - +
182A PHE* 1.3 57.8 + - - +
183A TRP* 3.4 4.9 - - - +
184A PHE* 3.7 29.6 + - + +
185A LYS* 3.9 12.9 + - + +
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Residues in contact with PHE 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 VAL* 2.9 34.7 + - + +
179A SER* 3.8 17.0 - - - -
180A SER 3.8 0.4 - - - -
181A ASN* 1.3 73.4 - - - +
183A TRP* 1.3 66.4 + - - +
184A PHE 3.1 1.2 + - - -
185A LYS* 3.7 11.4 + - - +
186A TYR* 3.8 25.9 + + - +
307A LEU* 4.7 19.6 - - + +
310A VAL* 6.2 1.6 - - + -
311A GLN* 4.2 22.4 - - + -
314A ILE* 5.1 7.6 - - + -
27B PHE* 5.7 11.4 - + - -
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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
------------------------------------------------------------
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