Contacts of the helix formed by residues 165 - 185 (chain A) in PDB entry 4PK7
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ALA* 1.3 79.4 - - - +
166A PRO* 1.3 74.5 - - - +
167A GLN* 3.3 8.5 - - - -
168A TRP 4.1 0.4 - - - -
169A LYS* 3.3 21.0 + - - +
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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
----------------------------------------------------------
165A GLY* 1.3 84.3 - - - +
167A GLN* 1.3 63.1 + - - +
168A TRP 3.2 0.2 - - - -
169A LYS* 3.7 8.0 - - + +
170A LYS* 2.8 47.9 + - - +
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 4.0 29.4 - - - +
164A ALA 4.5 3.2 + - - -
165A GLY* 3.4 8.0 - - - -
166A PRO* 1.3 89.1 - - - +
168A TRP* 1.3 75.6 + - + +
170A LYS* 4.0 13.1 - - + +
171A PHE* 3.4 17.8 + - - +
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Residues in contact with TRP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 5.1 7.4 - + - -
89A LYS* 3.6 38.1 - - + -
160A PRO* 3.8 32.6 - - + +
163A MET* 3.4 58.2 - - + +
164A ALA 3.2 22.4 - - - +
165A GLY 3.7 4.6 + - - +
166A PRO 3.2 0.2 - - - -
167A GLN* 1.3 93.2 + - - +
169A LYS* 1.3 61.6 + - - +
170A LYS 3.2 1.1 - - - -
171A PHE* 2.9 25.1 + + + +
172A LYS* 2.9 29.6 + - - +
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Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 3.3 16.7 + - - +
166A PRO* 3.7 8.5 - - + +
168A TRP* 1.3 76.7 - - - +
170A LYS* 1.3 64.4 + - + +
171A PHE 3.3 0.3 + - - -
172A LYS* 3.5 7.5 + - + +
173A SER* 3.3 22.5 + - - -
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Residues in contact with LYS 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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89A LYS* 5.9 1.1 - - - +
92A LYS* 3.9 31.4 - - - +
166A PRO* 2.8 36.3 + - - +
167A GLN* 4.0 11.4 - - + +
168A TRP 3.2 0.2 - - - -
169A LYS* 1.3 75.4 - - + +
171A PHE* 1.3 61.9 + - - +
173A SER* 3.1 8.1 + - - -
174A SER* 3.0 28.2 + - - +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.0 27.4 - + - -
88A VAL* 5.0 6.1 - - + -
89A LYS* 3.4 37.0 - - + +
124A CYS* 4.1 27.6 - - + -
160A PRO* 3.5 28.0 - - + -
161A LEU* 4.6 12.3 - - + -
167A GLN 3.4 14.3 + - - +
168A TRP* 2.9 30.4 + + + +
170A LYS* 1.3 76.4 - - - +
172A LYS* 1.3 80.8 + - + +
174A SER* 2.9 5.8 + - - -
175A PHE* 2.8 33.9 + + + +
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Residues in contact with LYS 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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160A PRO 6.0 0.4 - - - +
161A LEU* 3.9 31.9 - - + +
168A TRP 2.9 17.2 + - - +
169A LYS* 3.5 7.4 + - + +
171A PHE* 1.3 80.0 - - + +
173A SER* 1.3 63.1 + - - +
175A PHE* 3.4 6.5 - - - +
176A CYS* 3.1 29.1 + - - -
221A LEU* 4.4 20.9 - - + -
307A ILE* 6.2 2.8 - - - +
310A GLU* 6.0 0.4 + - - -
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Residues in contact with SER 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 LYS* 3.3 12.2 + - - -
170A LYS* 3.1 16.3 + - - -
171A PHE 3.1 0.2 - - - -
172A LYS* 1.3 78.3 - - - +
174A SER* 1.3 59.3 + - - +
176A CYS* 3.3 6.3 + - - +
177A GLU* 2.9 31.3 + - - +
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Residues in contact with SER 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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88A VAL* 3.3 35.9 + - - +
89A LYS* 5.2 0.7 - - - -
95A MET* 3.8 11.8 - - - +
170A LYS* 3.0 16.5 + - - +
171A PHE* 2.9 8.3 + - - -
173A SER* 1.3 74.0 + - - +
175A PHE* 1.3 65.8 + - - +
177A GLU* 4.3 4.7 - - - -
178A PHE* 3.0 25.5 + - - +
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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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88A VAL* 3.8 7.7 - - - +
120A PHE* 3.9 17.3 - + - -
121A PHE* 4.1 4.7 - + - -
124A CYS* 3.5 41.5 - - + -
161A LEU* 5.1 4.5 - - + -
171A PHE* 2.8 24.5 + + + +
172A LYS* 3.4 10.3 - - - +
174A SER* 1.3 78.3 - - - +
176A CYS* 1.3 67.3 + - - +
178A PHE* 3.4 5.6 + - - +
179A ILE* 3.3 46.6 + - + +
218A THR* 4.1 14.6 - - + -
221A LEU* 3.8 32.5 - - + -
222A ALA* 3.7 21.3 - - + -
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Residues in contact with CYS 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 LYS* 3.1 25.6 + - - +
173A SER* 3.3 5.8 + - - +
175A PHE* 1.3 80.2 - - - +
177A GLU* 1.3 65.0 + - - +
179A ILE* 3.6 4.1 + - - +
180A GLY* 3.2 18.0 + - - -
221A LEU* 3.9 24.5 - - - -
225A LYS* 3.3 50.0 - - + +
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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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95A MET* 3.6 25.0 - - + +
173A SER 2.9 18.1 + - - +
174A SER* 3.8 7.0 - - - +
176A CYS* 1.3 76.9 - - - +
178A PHE* 1.3 57.3 + - - +
180A GLY* 3.3 1.8 + - - -
181A VAL* 2.8 50.3 + - + +
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Residues in contact with PHE 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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84A LEU* 4.2 18.2 - - + -
88A VAL* 4.8 6.1 - - + -
95A MET* 3.5 31.6 - - + +
98A VAL* 4.2 18.8 - - + -
99A VAL* 3.7 25.2 - - + +
102A TRP* 5.1 6.1 - - + -
117A LEU* 4.1 16.2 - - + -
120A PHE* 4.0 33.7 - + + -
121A PHE* 5.9 0.9 - + - -
174A SER 3.0 18.8 + - - +
175A PHE* 3.6 5.6 - - - +
176A CYS 3.3 0.2 - - - -
177A GLU* 1.3 77.8 - - - +
179A ILE* 1.3 62.8 + - + +
181A VAL* 4.7 1.6 - - - -
182A LEU* 2.9 52.1 + - + +
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Residues in contact with ILE 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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120A PHE* 5.1 0.2 - - + -
121A PHE* 3.7 21.3 - - + -
175A PHE* 3.3 32.3 + - + +
176A CYS* 4.0 6.1 - - - +
177A GLU 3.3 0.6 - - - -
178A PHE* 1.3 86.6 - - + +
180A GLY* 1.3 64.5 + - - +
182A LEU* 3.7 4.8 - - + +
183A VAL* 3.3 22.7 + - - +
204A LEU* 6.2 0.2 - - + -
222A ALA* 3.5 38.6 - - + +
225A LYS* 3.9 7.0 - - + -
226A LEU* 3.6 42.4 - - + +
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Residues in contact with GLY 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 CYS 3.2 11.9 + - - -
177A GLU 3.7 2.7 - - - -
179A ILE* 1.3 82.6 - - - +
181A VAL* 1.3 61.1 + - - +
182A LEU 3.2 0.7 + - - -
183A VAL* 3.2 1.6 + - - +
184A ARG* 3.1 51.9 + - - +
225A LYS* 5.1 3.1 - - - +
229A ALA* 4.0 6.5 - - - -
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Residues in contact with VAL 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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95A MET* 4.4 4.9 - - + +
96A GLN* 4.0 27.4 - - + +
99A VAL* 3.6 23.5 - - + +
177A GLU* 2.8 46.9 + - + +
178A PHE* 4.3 1.1 - - - +
180A GLY* 1.3 71.2 - - - -
182A LEU* 1.3 59.6 + - - +
184A ARG* 4.6 10.5 - - - +
185A GLN* 3.1 32.2 + - + +
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Residues in contact with LEU 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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99A VAL* 3.7 25.5 - - + +
102A TRP* 3.7 30.5 - - + -
103A ILE* 4.4 0.4 - - + -
117A LEU* 4.0 26.9 - - + -
121A PHE* 6.4 1.3 - - + -
178A PHE* 2.9 33.8 + - + +
179A ILE* 3.7 6.7 - - + +
180A GLY 3.1 0.4 - - - -
181A VAL* 1.3 74.9 - - - +
183A VAL* 1.3 67.0 + - + +
185A GLN* 3.5 2.8 + - - +
186A CYS* 3.2 36.1 + - - -
196A MET* 4.0 21.5 - - + -
200A VAL* 6.1 0.2 - - + -
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Residues in contact with VAL 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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179A ILE 3.4 11.4 - - - +
180A GLY 3.2 1.0 + - - +
182A LEU* 1.3 77.2 - - + +
184A ARG* 1.3 60.2 + - - +
186A CYS* 2.8 26.4 + - - +
187A GLN* 3.2 11.8 + - - +
191A ILE* 4.1 16.1 - - + +
196A MET* 6.2 1.6 - - + -
197A MET* 4.7 9.6 - - - -
226A LEU* 3.3 32.3 - - + -
229A ALA* 3.6 33.7 - - + -
230A LEU* 4.2 7.2 - - + -
233A VAL* 4.1 13.9 - - + -
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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
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180A GLY* 3.1 43.8 + - - +
181A VAL* 4.3 9.4 - - - +
183A VAL* 1.3 77.2 - - - +
185A GLN* 1.3 64.6 + - - +
186A CYS 3.2 1.0 + - - -
187A GLN* 3.0 41.2 + - - +
188A TYR* 5.1 2.1 - - - -
225A LYS 5.3 0.2 + - - -
228A THR* 4.1 15.6 + - - +
229A ALA* 3.4 35.2 - - - +
232A ASN* 4.0 30.8 - - - +
233A VAL* 5.1 1.3 - - + -
318A MET* 5.1 4.0 - - - -
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Residues in contact with GLN 185 (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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96A GLN* 3.6 31.5 + - + -
99A VAL* 3.9 10.5 - - + -
100A ASP* 3.3 17.9 - - - +
103A ILE* 3.4 30.1 - - + +
181A VAL* 3.1 29.0 + - + +
182A LEU 3.7 0.9 - - - +
183A VAL 3.2 0.2 - - - -
184A ARG* 1.3 78.8 + - + +
186A CYS* 1.3 57.3 + - - +
187A GLN 3.6 0.4 - - - -
188A TYR* 6.3 1.3 - - - -
190A ILE* 5.6 0.5 - - - +
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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