Contacts of the strand formed by residues 164 - 177 (chain C) in PDB entry 3IML
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 LEU 164 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLN* 3.6 33.0 - - + +
155C LEU* 4.0 7.9 - - + -
156C ARG* 3.4 37.0 - - + +
161C LEU* 3.2 38.6 + - + +
162C PRO 4.1 5.4 - - - +
163C TRP* 1.3 101.1 - - + +
165C ARG* 1.3 63.7 + - - +
191C THR* 3.3 31.6 - - + +
192C GLN 4.0 1.6 - - - +
206C VAL* 5.1 3.4 - - + -
210C VAL* 5.3 1.6 - - + -
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLN* 3.4 18.5 + - - -
156C ARG* 3.4 7.6 - - - +
163C TRP 4.0 0.7 - - - +
164C LEU* 1.3 78.1 - - - +
166C PRO* 1.3 77.6 - - + +
167C ASP 3.4 5.4 + - - +
192C GLN* 3.1 38.6 + - + +
193C HIS 3.6 18.1 + - - -
194C ALA* 3.6 20.6 - - + +
195C PRO* 3.7 17.8 - - - +
196C GLU* 5.3 0.2 + - - -
235C VAL* 3.2 31.5 + - - +
236C ILE* 5.2 3.2 - - - +
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Residues in contact with PRO 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 2.6 29.5 + - - -
14C GLU* 5.3 0.2 - - - +
15C GLY* 3.8 8.9 + - - -
77C ILE 3.7 24.5 - - - +
78C GLY* 3.9 20.0 - - - +
79C TYR* 3.6 31.4 - - + -
152C GLN* 3.9 5.9 - - - +
156C ARG* 3.5 20.0 + - - +
165C ARG* 1.3 93.9 - - + +
167C ASP* 1.3 52.9 + - - +
192C GLN* 3.6 6.5 - - - +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.5 2.9 - - - -
15C GLY 3.7 8.7 - - - -
16C HIS* 3.5 26.0 - - - +
17C PRO* 3.8 7.0 - - - +
79C TYR* 3.5 8.7 - - - +
165C ARG 3.7 1.7 - - - +
166C PRO* 1.3 77.9 - - - +
168C ALA* 1.3 71.3 + - - +
192C GLN* 2.9 49.5 + - + +
234C PHE* 3.7 16.5 - - + -
237C GLY* 3.4 5.0 - - - -
238C GLY* 2.7 24.3 + - - +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.4 4.5 - - - +
13C SER* 2.8 37.5 + - - -
16C HIS* 5.2 0.4 - - - -
149C VAL* 4.2 4.9 - - + -
152C GLN* 3.4 38.6 - - + +
167C ASP* 1.3 86.4 + - - +
169C LYS* 1.3 59.2 + - - +
189C LEU* 5.2 2.5 - - + -
190C SER 3.2 14.6 - - - +
191C THR* 4.1 2.9 - - - +
234C PHE* 4.8 2.0 - - - -
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 4.1 14.5 + - - +
11C SER 3.6 10.8 - - - +
12C VAL* 4.0 15.3 - - + +
16C HIS* 3.9 23.2 + - + -
149C VAL* 4.0 3.6 - - - -
168C ALA* 1.3 74.1 - - - +
170C SER* 1.3 65.0 + - - +
188C VAL* 4.6 1.1 - - - +
189C LEU* 3.5 5.9 - - - +
190C SER* 2.8 43.1 + - - +
234C PHE* 5.4 2.4 - - + -
249C LYS* 4.9 7.0 - - - +
123D GLN* 3.9 37.3 + - + +
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 3.2 5.6 - - - +
11C SER* 2.8 39.8 + - - +
145C SER* 2.5 36.2 + - - -
148C LEU* 3.9 21.3 - - - -
149C VAL* 3.6 11.6 - - - +
169C LYS* 1.3 76.4 - - - +
171C GLN* 1.3 61.4 + - - +
188C VAL* 3.4 8.1 - - - -
189C LEU* 4.6 3.6 - - - +
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Residues in contact with GLN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 3.4 19.6 - - + +
9C SER 3.5 6.5 - - - +
10C GLU* 3.0 26.6 - - + +
145C SER* 4.5 0.2 - - - -
169C LYS* 6.0 0.4 - - + -
170C SER* 1.3 76.0 - - - +
172C VAL* 1.3 62.6 + - - +
173C THR* 5.3 1.3 - - - +
186C THR* 3.8 1.2 - - - +
187C VAL* 3.5 2.9 - - - -
188C VAL* 2.8 57.0 + - + +
123D GLN* 3.2 12.3 - - + +
124D GLY* 3.0 22.3 + - - +
125D LEU* 4.4 0.9 - - - -
303D SER* 3.1 18.8 + - - -
304D TYR 2.7 29.7 + - - +
305D ALA* 5.4 0.2 - - - -
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE 3.7 1.4 - - - +
8C THR* 3.2 3.0 - - - -
9C SER 2.9 32.7 + - - -
141C PRO* 4.0 10.3 - - - +
144C LEU* 4.2 18.4 - - + -
145C SER* 3.5 27.4 - - - +
148C LEU* 3.7 28.7 - - + -
171C GLN* 1.3 77.0 - - - +
173C THR* 1.3 65.7 + - - +
174C VAL* 4.0 19.9 + - + -
184C ILE* 4.4 11.9 - - + -
186C THR 3.5 6.3 - - - +
187C VAL* 4.7 5.4 - - + -
215C LEU* 5.9 0.2 - - + -
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.9 29.8 - - + -
7C PHE 3.5 4.9 - - - +
8C THR* 2.7 28.6 + - - +
171C GLN* 4.3 1.6 - - - +
172C VAL* 1.3 71.2 - - - +
174C VAL* 1.3 62.6 + - - +
184C ILE* 3.8 5.2 - - - +
185C ASP* 2.9 39.7 + - + +
186C THR* 2.8 33.5 + - - +
303D SER* 4.8 1.0 + - - -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.5 4.4 - - - -
7C PHE 2.9 32.2 + - - +
140C LEU* 4.2 17.5 - - + -
141C PRO* 3.9 23.6 - - + -
144C LEU* 5.5 0.2 - - + -
172C VAL* 4.1 15.7 - - + -
173C THR* 1.3 75.5 - - - +
175C ARG* 1.3 72.7 + - - +
176C TYR* 3.6 25.9 + - + -
181C PRO* 4.2 19.5 - - + -
183C SER 3.4 14.1 - - - +
184C ILE* 4.6 5.8 - - + +
219C LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 2.8 41.1 + - - +
5C TYR 3.7 4.9 - - - +
6C LEU* 3.8 21.9 - - + +
173C THR 4.2 0.8 + - - -
174C VAL* 1.3 74.6 - - - +
176C TYR* 1.3 58.9 + - - +
177C VAL* 3.7 15.2 - - + +
182C HIS* 3.0 44.7 + - - +
183C SER* 2.9 33.2 + - - +
185C ASP* 4.4 3.9 - - + +
223C ASP* 5.3 8.9 + - - -
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 3.3 6.6 + - - +
5C TYR* 2.8 66.2 + + + +
7C PHE* 3.8 26.5 - + + -
133C GLU* 2.7 40.3 + - - -
139C PRO* 5.2 0.5 - - - +
140C LEU* 4.4 0.2 - - - +
141C PRO* 3.3 19.4 - - + +
174C VAL* 3.7 28.3 - - + -
175C ARG* 1.3 72.1 - - - +
177C VAL* 1.3 61.3 + - - +
178C ASP 4.2 0.4 + - - -
179C GLY 3.9 12.6 - - - +
180C LYS 3.5 19.7 - - - +
181C PRO* 3.6 19.7 - - + +
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP* 3.7 23.6 - - + +
175C ARG* 3.7 16.7 + - - +
176C TYR* 1.3 74.7 - - - +
178C ASP* 1.3 85.6 - - - +
179C GLY 3.3 0.7 - - - -
180C LYS* 3.1 20.8 + - - +
182C HIS* 3.6 40.6 - - + +
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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