Contacts of the helix formed by residues 167 - 185 (chain A) in PDB entry 4KZX
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 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 4.9 9.2 - - - -
164A ASN* 3.0 11.0 + - - +
165A ASN* 3.0 8.5 - - - -
166A LYS* 1.3 81.2 - - - +
168A ALA* 1.3 73.0 + - - +
170A SER* 2.3 31.0 + - - -
171A VAL* 3.5 9.7 + - - -
204A TYR* 5.0 0.2 - - - -
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 4.8 5.4 - - - +
82A THR* 5.1 1.6 - - - +
167A GLY* 1.3 75.8 - - - +
169A HIS* 1.3 79.1 + - + +
170A SER* 4.2 1.3 - - - +
171A VAL* 4.3 5.2 + - - +
172A GLY 4.3 4.5 + - - -
203A PHE* 5.2 3.5 - - - -
204A TYR* 3.6 44.0 + - - +
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Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 4.0 20.0 + - + -
168A ALA* 1.3 94.1 - - + +
170A SER* 1.3 54.9 + - - +
171A VAL 3.2 2.7 - - - -
172A GLY 3.5 0.9 - - - -
173A LEU* 2.6 37.7 + - + +
203A PHE* 2.9 48.9 - + + -
204A TYR* 5.1 7.0 - + - -
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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
----------------------------------------------------------
21A ALA 3.6 18.1 + - - -
22A GLY 4.1 1.3 - - - -
23A THR* 3.9 18.7 - - - +
163A CYS* 5.0 2.6 - - - +
164A ASN* 3.5 33.2 + - - +
165A ASN 3.7 7.1 + - - -
167A GLY 2.3 27.0 + - - -
168A ALA* 5.4 0.2 - - - -
169A HIS* 1.3 79.5 - - - +
171A VAL* 1.3 60.3 + - - +
174A MET* 3.0 31.4 + - - +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.4 1.1 - - - +
82A THR* 3.7 37.5 - - - +
83A GLY* 3.8 15.5 - - - -
86A ALA* 4.7 0.4 - - + -
125A THR* 5.0 3.1 - - - -
147A LEU* 4.1 19.7 - - + -
163A CYS* 5.9 0.4 - - + -
165A ASN* 3.9 29.4 - - + +
167A GLY* 3.5 8.4 + - - +
168A ALA 4.8 1.6 - - - +
169A HIS 3.2 0.2 - - - -
170A SER* 1.3 80.6 + - - +
172A GLY* 1.3 68.5 + - - +
174A MET* 4.3 2.5 - - - +
175A TRP* 3.4 36.4 + - + +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR 4.9 1.8 + - - -
86A ALA* 4.9 4.0 - - - -
168A ALA 4.3 2.2 + - - -
169A HIS* 3.1 5.9 + - - +
171A VAL* 1.3 81.3 - - - +
173A LEU* 1.3 61.8 + - - +
175A TRP* 3.5 0.9 + - - +
176A TRP* 3.0 22.7 + - - +
202A TYR* 3.7 11.9 - - - +
203A PHE* 3.2 37.2 - - - -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.1 27.1 - - + +
18A PHE* 4.4 5.8 - - + +
21A ALA* 1.8 48.9 - - + -
23A THR* 4.6 5.8 - - + -
169A HIS 2.6 16.5 + - - +
170A SER 4.2 2.7 - - - +
172A GLY* 1.3 73.1 - - - +
174A MET* 1.3 55.1 + - + +
176A TRP* 3.2 8.7 - - + +
177A MET* 2.7 46.8 + - + +
199A PRO* 4.0 22.0 - - + -
203A PHE* 3.6 20.9 - - + -
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.7 30.5 - - - -
23A THR* 4.2 12.6 - - + -
54A THR* 3.5 19.3 - - + -
58A LEU* 3.8 17.3 - - + +
147A LEU* 5.0 4.7 - - + -
161A ILE* 2.9 38.4 - - + -
162A PRO 4.2 2.7 - - - +
163A CYS* 3.9 19.1 - - + -
170A SER 3.0 23.3 + - - +
171A VAL* 4.3 3.4 - - - +
172A GLY 3.2 0.8 - - - -
173A LEU* 1.3 74.2 - - - +
175A TRP* 1.3 58.0 + - + +
177A MET* 4.1 3.2 - - - +
178A LEU* 2.8 41.6 + - + +
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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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76A VAL* 2.6 50.9 - - + -
86A ALA* 4.0 12.8 - - + -
87A VAL* 3.7 5.7 - - + +
90A PHE* 3.8 28.9 - + + -
123A VAL* 3.0 39.7 - - + -
124A VAL 4.6 1.1 - - - -
125A THR* 2.7 39.2 - - + +
147A LEU* 4.8 6.8 - - + +
171A VAL* 3.4 34.3 + - + +
174A MET* 1.3 77.4 - - + +
176A TRP* 1.3 63.5 + - - +
178A LEU* 3.3 14.9 + - + +
179A ALA* 3.0 24.4 + - - +
202A TYR* 3.8 20.5 - - + -
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Residues in contact with TRP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 5.7 8.7 - - + -
172A GLY 3.0 15.0 + - - +
173A LEU* 3.2 15.3 - - + +
175A TRP* 1.3 74.4 - - - +
177A MET* 1.3 111.7 + - + +
179A ALA* 3.3 2.3 + - - +
180A ARG* 2.8 50.9 + - + +
194A PRO 5.9 0.4 - - - -
195A TRP* 1.7 78.4 - + + -
197A VAL* 3.7 5.5 + - + +
198A MET 4.1 1.7 - - - -
199A PRO* 3.2 46.0 - - + +
202A TYR* 3.6 25.6 - + + -
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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
----------------------------------------------------------
14A ASP* 3.7 3.6 - - + +
17A LYS* 5.5 7.2 - - + -
18A PHE* 3.8 18.4 - - + -
55A TRP* 3.5 23.8 - - + -
58A LEU* 3.5 20.9 - - + -
173A LEU* 2.7 33.8 + - + +
174A MET 4.1 0.4 - - - +
176A TRP* 1.3 115.2 - - + +
178A LEU* 1.3 54.6 + - - +
180A ARG* 1.9 42.8 - - - +
181A GLU* 2.7 42.0 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.0 52.7 - - + +
61A ALA* 4.2 11.9 - - + -
62A ALA* 4.7 3.6 - - - +
65A ILE* 5.0 9.2 - - + -
90A PHE* 4.3 8.7 - - + -
123A VAL* 4.9 9.6 - - + -
145A ILE* 5.7 0.7 - - + -
161A ILE* 4.9 9.6 - - + -
174A MET* 2.8 28.0 + - + +
175A TRP* 3.5 28.5 - - + +
176A TRP 3.1 0.4 - - - -
177A MET* 1.3 73.6 - - - +
179A ALA* 1.3 56.7 + - - +
181A GLU* 3.0 4.3 + - - +
182A VAL* 2.7 42.1 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.5 19.2 - - + -
93A ALA* 4.7 7.9 - - + -
94A THR* 4.6 5.2 - - + -
175A TRP 3.0 5.2 + - - +
176A TRP 3.7 6.3 - - - +
178A LEU* 1.3 77.0 - - - +
180A ARG* 1.3 61.5 + - - +
182A VAL* 3.1 10.9 - - + +
183A LEU* 2.9 35.3 + - + +
195A TRP* 4.7 4.3 - - + -
202A TYR* 3.4 26.0 - - + +
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Residues in contact with ARG 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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11A LYS* 3.7 1.4 - - - +
14A ASP* 2.5 33.9 + - - -
17A LYS* 5.9 0.2 - - - +
55A TRP* 3.9 0.6 - - - -
176A TRP* 2.8 35.2 + - + +
177A MET* 1.9 47.9 - - - +
179A ALA* 1.3 73.6 - - - +
181A GLU* 1.3 69.1 + - - +
184A ARG* 2.4 97.9 - - - +
189A ILE* 3.1 16.6 - - + +
194A PRO* 5.5 2.0 - - - +
195A TRP* 4.0 36.5 - - + +
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Residues in contact with GLU 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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55A TRP* 3.9 9.1 - - - -
58A LEU* 5.0 4.5 - - + +
59A LEU* 2.9 37.7 - - + +
62A ALA* 3.5 19.5 - - + -
177A MET* 2.7 29.1 + - - +
178A LEU* 3.4 5.4 - - - +
180A ARG* 1.3 92.5 + - - +
182A VAL* 1.3 64.6 + - - +
184A ARG* 2.9 40.0 + - - +
185A MET* 3.1 27.3 + - + +
192A GLU* 5.2 3.8 - - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.6 32.5 - - - +
65A ILE* 3.8 28.7 - - + -
66A VAL* 3.7 11.3 - - + +
90A PHE* 4.2 2.2 - - + -
94A THR* 2.8 38.6 - - + -
178A LEU 2.7 22.5 + - - +
179A ALA* 3.1 12.6 - - - +
181A GLU* 1.3 70.9 - - - +
183A LEU* 1.3 59.2 + - - +
185A MET* 2.7 28.2 + - - +
186A ARG 3.2 9.2 - - - +
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Residues in contact with LEU 183 (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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93A ALA* 4.1 33.0 - - + +
94A THR* 3.9 21.1 - - + -
179A ALA 2.9 26.9 + - - +
182A VAL* 1.3 79.0 - - - +
184A ARG* 1.3 57.6 + - - +
187A GLY* 3.2 9.2 - - - -
188A THR* 2.8 32.7 + - + +
189A ILE* 2.8 31.6 + - + -
195A TRP* 4.7 16.2 - - + +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.4 20.5 - - - +
14A ASP* 4.7 0.4 + - - -
55A TRP* 5.2 2.6 - - - -
180A ARG* 2.4 73.9 - - - +
181A GLU* 2.9 28.3 + - - +
182A VAL 3.2 0.2 - - - -
183A LEU* 1.3 75.9 - - - +
185A MET* 1.3 67.6 + - + +
187A GLY 4.3 1.2 + - - -
188A THR* 4.5 3.1 + - - -
189A ILE* 3.2 26.2 + - + +
190A SER* 4.5 6.9 + - - +
192A GLU* 3.8 45.1 + - + +
193A HIS 4.0 16.9 + - - -
194A PRO* 4.2 8.9 - - - +
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Residues in contact with MET 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.4 7.2 - - - -
62A ALA* 5.4 1.8 - - + -
63A ARG* 3.6 46.0 - - + +
66A VAL* 3.6 25.1 - - + -
181A GLU* 3.1 14.3 + - + +
182A VAL* 2.7 11.8 - - - +
184A ARG* 1.3 81.6 - - + +
186A ARG* 1.3 79.8 - - - +
187A GLY 2.3 4.7 + - - -
192A GLU* 4.3 16.4 + - - +
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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
------------------------------------------------------------
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