Contacts of the helix formed by residues 160 - 177 (chain T) in PDB entry 5GJQ
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 ASP 160 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T SER* 6.0 0.2 - - - -
155T SER* 3.0 14.9 + - - +
158T ARG* 3.0 39.0 - - + -
159T LYS* 1.3 73.2 - - - +
161T ILE* 1.3 62.1 + - - +
162T PRO* 3.5 5.8 - - - -
163T SER* 2.1 45.2 + - - +
164T PHE* 3.4 1.9 + - - -
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Residues in contact with ILE 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156T ILE* 5.2 4.5 - - - +
159T LYS* 2.9 21.3 + - - +
160T ASP* 1.3 75.2 - - - +
162T PRO* 1.4 64.7 - - - +
164T PHE* 2.9 45.0 + - + -
165T GLU* 3.1 12.5 + - + +
198T PHE* 5.9 3.1 - - + -
202T GLN* 5.2 13.9 - - + +
259T PHE* 4.6 22.0 - - + -
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Residues in contact with PRO 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N ASP* 6.5 0.4 - - - -
159T LYS 5.8 0.4 - - - +
160T ASP 4.2 5.6 - - - +
161T ILE* 1.4 74.5 - - - +
163T SER* 1.3 73.6 + - - +
165T GLU* 2.9 39.4 + - - +
166T ARG* 3.0 11.5 + - + +
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Residues in contact with SER 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N ASP* 6.6 0.4 - - - -
14N GLU* 5.8 4.3 - - - -
155T SER* 3.8 7.1 + - - -
160T ASP* 2.1 46.6 + - - +
162T PRO* 1.3 79.0 - - - +
164T PHE* 1.3 61.0 + - - -
166T ARG* 2.6 35.7 + - - +
167T TYR* 2.8 21.9 + - - -
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Residues in contact with PHE 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152T ALA* 3.5 39.2 - - + +
155T SER* 3.6 19.7 - - - -
156T ILE* 4.5 13.7 - - + -
161T ILE* 2.9 46.7 + - + -
163T SER* 1.3 79.0 + - - +
165T GLU* 1.3 64.5 + - + +
167T TYR* 3.1 13.4 - - + -
168T MET* 2.2 44.4 + - + +
191T LEU* 5.2 3.6 - - + -
194T LEU* 4.8 16.4 - - + -
195T ASN* 5.0 11.4 - - + -
198T PHE* 3.6 31.6 - + - -
259T PHE* 5.1 2.7 - + - -
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Residues in contact with GLU 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161T ILE* 3.1 15.3 + - - +
162T PRO* 2.9 28.8 + - - +
164T PHE* 1.3 85.5 - - + +
166T ARG* 1.3 49.5 + - + +
168T MET* 2.9 8.9 + - - +
169T ALA* 2.3 40.8 + - - +
195T ASN* 5.5 8.3 - - - -
198T PHE* 5.2 7.9 - - + +
199T LEU* 4.2 20.2 - - + +
202T GLN* 5.2 8.3 - - - +
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Residues in contact with ARG 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA 4.4 0.9 - - - -
9N ILE* 4.4 6.1 - - + +
10N SER* 2.7 44.6 - - - +
13N ASP* 5.7 8.5 - - + -
14N GLU* 5.1 0.4 - - - +
162T PRO 3.0 11.9 + - - +
163T SER* 2.6 21.9 + - - +
165T GLU* 1.3 72.6 - - + +
167T TYR* 1.3 49.9 + - + +
169T ALA* 2.9 9.9 + - - +
170T GLN* 2.4 39.2 + - - +
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Residues in contact with TYR 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER* 4.6 0.2 - - - -
14N GLU* 2.9 31.5 + - - +
109T LEU* 3.4 24.7 - - + +
148T LEU* 3.7 29.2 - - + +
151T GLY* 3.7 23.8 - - - -
152T ALA* 4.7 2.7 - - + -
155T SER* 3.4 17.9 - - - -
163T SER* 2.8 26.7 + - - -
164T PHE* 2.9 27.8 + - + +
166T ARG* 1.3 69.6 - - - +
168T MET* 1.3 51.8 + - - +
170T GLN* 2.9 23.1 + - - +
171T LEU* 2.4 43.3 + - + +
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Residues in contact with MET 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152T ALA* 5.6 0.2 - - - +
164T PHE* 2.2 37.9 + - + +
165T GLU* 3.2 9.9 - - - +
167T TYR* 1.3 66.6 - - - +
169T ALA* 1.3 64.6 + - - +
171T LEU* 2.9 16.6 + - + +
172T LYS* 2.8 35.6 + - + +
191T LEU* 5.7 9.6 - - + -
192T LEU* 5.9 7.0 - - + -
195T ASN* 4.0 28.0 - - + -
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Residues in contact with ALA 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA* 2.7 32.3 - - + +
9N ILE* 5.5 2.9 - - + -
165T GLU 2.3 27.2 + - - +
166T ARG* 3.1 14.1 - - - +
168T MET* 1.3 65.6 - - - +
170T GLN* 1.3 56.9 + - - +
172T LYS* 2.9 47.6 + - + +
173T CYS* 4.4 1.7 + - - -
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Residues in contact with GLN 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N ALA* 3.0 9.6 - - - +
7N GLY* 2.4 66.1 + - - +
10N SER* 2.9 13.7 - - - -
11N LEU* 3.7 10.7 - - - +
14N GLU* 4.5 2.6 + - - -
148T LEU* 3.8 20.6 - - + +
166T ARG 2.4 12.0 + - - +
167T TYR* 3.0 38.3 - - - +
169T ALA* 1.3 72.1 - - - +
171T LEU* 1.3 58.6 + - - +
172T LYS 3.4 0.7 + - - -
173T CYS* 4.1 7.8 - - - -
174T TYR* 3.0 23.9 - - + -
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Residues in contact with LEU 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145T ARG* 3.9 20.2 - - - +
148T LEU* 3.6 36.3 - - + +
149T GLU* 4.4 8.7 - - + +
152T ALA* 5.1 1.6 - - + -
167T TYR* 2.4 38.6 + - + +
168T MET* 2.9 17.2 + - + +
170T GLN* 1.3 70.1 - - - +
172T LYS* 1.3 63.5 + - - +
173T CYS 3.4 0.2 - - - -
174T TYR* 2.8 29.7 + - + +
175T TYR* 3.6 28.5 + - + -
191T LEU* 3.9 28.3 - - + -
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Residues in contact with LYS 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA* 5.3 1.3 - - + -
263S LEU* 6.1 5.2 - - + -
265S ASP* 5.8 2.2 + - - -
165T GLU 5.5 0.2 - - - -
168T MET* 2.8 25.1 + - + +
169T ALA* 2.9 36.4 + - + +
171T LEU* 1.3 75.7 - - - +
173T CYS* 1.3 64.9 + - - +
174T TYR 3.0 1.0 + - - -
175T TYR* 3.6 1.7 + - - -
176T PHE* 2.9 49.5 + - + +
211T GLU* 4.4 23.2 + - - -
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Residues in contact with CYS 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N THR* 4.8 13.2 - - + -
4N SER* 4.0 36.1 - - - -
6N ALA* 5.3 1.3 - - - -
125T GLU 5.2 6.5 - - - +
126T LEU* 5.7 4.9 - - + +
169T ALA 4.4 6.7 - - - -
170T GLN 4.1 12.8 - - - -
171T LEU 3.4 0.2 - - - -
172T LYS* 1.3 74.7 - - - +
174T TYR* 1.3 58.1 + - + +
176T PHE* 4.9 2.7 - - - -
177T ASP* 2.5 50.2 + - + +
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Residues in contact with TYR 174 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123T LEU 4.3 2.6 + - - -
124T LEU* 5.2 4.0 - - - -
125T GLU 5.5 0.7 + - - -
126T LEU* 3.1 44.2 - - + +
141T LEU* 4.4 9.0 - - + -
144T ALA* 4.8 11.4 - - + +
145T ARG* 3.4 36.3 - - + -
148T LEU* 4.8 12.4 - - + +
170T GLN 3.0 28.9 - - - -
171T LEU* 2.8 21.2 + - + +
173T CYS* 1.3 84.1 - - + +
175T TYR* 1.3 67.7 + - + +
177T ASP* 3.2 19.9 + - - +
182T LEU* 3.4 30.7 - - + +
183T PRO* 4.0 1.6 - - - +
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Residues in contact with TYR 175 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145T ARG* 4.9 5.5 - - + +
149T GLU* 2.5 37.1 + - - +
171T LEU* 3.7 38.7 - - + +
172T LYS* 3.6 3.0 + - - +
174T TYR* 1.3 81.5 - - + +
176T PHE* 1.3 70.3 + + + +
177T ASP 3.5 1.6 + - - +
182T LEU 4.7 4.0 - - - -
183T PRO* 2.7 59.2 - - + +
185T SER* 2.7 19.6 + - - -
187T TYR 4.4 0.7 - - - -
188T MET* 3.3 39.5 + - + -
191T LEU* 5.3 2.8 - - + +
192T LEU* 5.5 6.5 - - + -
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Residues in contact with PHE 176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262S SER* 5.4 5.6 - - - -
172T LYS* 2.9 47.9 + - + +
173T CYS* 3.8 2.7 - - - -
175T TYR* 1.3 86.7 - + + +
177T ASP* 1.3 58.8 + - - +
178T TYR 3.9 1.0 + - - -
192T LEU* 6.0 4.9 - - + -
214T ARG* 4.1 19.3 - - + -
215T LEU* 3.4 45.8 - - + -
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Residues in contact with ASP 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126T LEU* 5.8 5.2 - - - +
173T CYS* 2.5 33.7 + - + +
174T TYR* 3.2 17.3 - - - +
175T TYR 3.5 3.2 - - - +
176T PHE* 1.3 79.0 - - - +
178T TYR* 1.3 73.3 + - + +
179T LYS* 2.9 11.6 + - - +
182T LEU* 3.3 26.0 - - - -
183T PRO* 5.3 0.9 - - - +
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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