Contacts of the strand formed by residues 163 - 171 (chain G) in PDB entry 1ILL
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 163 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU* 3.8 22.9 - - + -
133G TYR* 3.9 4.1 - + - -
135G THR* 2.7 33.2 + - + -
136G ASP 3.0 16.2 - - - -
137G TRP* 3.5 16.8 - + + +
154G LEU* 3.4 21.5 - - - +
156G SER* 3.5 23.7 + - - -
157G VAL* 3.7 31.4 - - + -
161G LYS 5.5 0.2 - - - +
162G ARG* 1.3 78.3 - - - +
164G THR* 1.4 61.1 + - - +
165G PHE* 3.7 26.7 - + - -
189G HIS* 2.8 26.0 + - - -
190G TRP* 2.9 28.9 + + + -
192G SER* 6.2 0.4 - - - -
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Residues in contact with THR 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G THR* 3.2 19.6 + - - -
136G ASP* 3.3 32.6 + - + +
163G TYR* 1.4 80.7 - - - +
165G PHE* 1.3 75.6 + - - +
188G ILE 2.7 24.6 + - - -
189G HIS* 4.1 9.8 - - - +
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Residues in contact with PHE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G LEU* 3.3 37.7 - - + -
106G LEU* 3.9 11.7 - - + -
133G TYR* 3.1 34.1 - - + -
134G ARG* 3.2 18.8 - - - +
135G THR* 4.2 3.1 - - - +
163G TYR* 3.7 23.8 - + - -
164G THR* 1.3 94.7 + - - +
166G ARG* 1.3 66.2 + - - +
167G VAL* 3.5 13.2 - - + -
186G HIS 4.0 0.3 - - - +
188G ILE* 3.1 54.4 + - + +
190G TRP* 4.1 14.4 - + + -
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Residues in contact with ARG 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G ARG* 3.0 40.7 + - - +
165G PHE* 1.3 79.5 - - - +
167G VAL* 1.3 65.4 + - - +
183G GLU* 2.6 44.5 + - - -
184G TRP* 3.5 31.2 - - + +
185G SER* 2.6 29.2 + - - -
186G HIS 3.2 22.3 - - - +
187G PRO* 3.2 22.3 - - + +
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G ALA* 4.2 4.8 - - + +
101G PRO* 6.2 0.7 - - + -
104G LEU* 3.8 30.3 - - + -
118G TRP* 4.7 0.4 - - - +
131G VAL* 3.3 33.9 - - + -
132G GLN 3.9 2.0 - - - +
133G TYR* 3.7 21.8 - - + -
165G PHE* 3.5 27.4 - - + -
166G ARG* 1.3 82.2 - - - +
168G ARG* 1.3 60.9 + - - +
169G SER 4.2 0.7 + - - -
184G TRP* 2.9 6.1 - - - +
185G SER* 2.7 47.5 + - - +
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Residues in contact with ARG 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ALA* 5.7 0.2 - - - -
101G PRO* 5.9 0.2 - - - -
131G VAL* 3.4 7.4 - - - +
132G GLN* 2.7 79.8 + - + +
167G VAL* 1.3 76.3 - - - +
169G SER* 1.4 73.9 - - - +
170G ARG* 5.0 1.8 - - + -
181G TRP* 3.3 43.4 - - + +
182G SER* 2.7 29.4 + - - +
183G GLU* 3.0 31.2 + - - +
184G TRP* 3.0 47.6 - - + +
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Residues in contact with SER 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G PRO* 2.6 27.5 + - - -
99G TRP 3.0 19.3 + - - -
100G ALA* 3.7 3.9 + - - +
101G PRO* 3.9 17.5 - - - -
122G PHE* 4.0 12.8 - - - -
130G LEU 4.0 5.6 - - - -
131G VAL* 4.4 2.9 - - - -
167G VAL 4.2 0.8 + - - -
168G ARG* 1.4 84.1 - - - +
170G ARG* 1.4 65.4 + - - +
182G SER* 3.5 22.2 + - - -
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Residues in contact with ARG 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194 GLU* 2.7 19.2 + - - -
98G PRO* 5.3 4.7 - - - +
122G PHE* 4.8 0.2 - - - -
127G LEU* 3.8 11.7 - - - +
130G LEU* 3.3 51.2 + - + +
132G GLN* 5.7 1.1 - - + +
147G ASP* 2.9 34.7 + - - -
168G ARG* 5.0 4.0 - - + +
169G SER* 1.4 75.9 - - - +
171G PHE* 1.4 79.1 + - - +
172G ASN* 3.4 18.4 + - - +
177G SER* 2.6 31.7 + - - -
178G ALA 5.3 0.2 - - - -
180G HIS 3.5 16.5 + - - +
181G TRP* 3.5 39.6 - - + +
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Residues in contact with PHE 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144 GLU* 3.8 17.7 - - + -
1214 ARG* 3.9 9.0 - - - -
10G ASN* 6.2 0.9 - - - -
11G VAL* 4.2 15.0 - - + -
96G VAL* 3.7 32.7 + - + -
98G PRO* 5.0 3.0 - - + +
126G CYS* 2.9 47.1 - - + -
127G LEU* 3.8 27.1 - - + +
128G GLU 4.6 0.9 - - - -
170G ARG* 1.4 74.8 - - - +
172G ASN* 1.3 68.6 + - - +
173G PRO* 4.3 8.5 - - + -
177G SER* 3.2 22.0 + - - -
178G ALA* 3.2 33.9 + - + +
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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
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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