Contacts of the strand formed by residues 164 - 177 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLN* 3.4 39.0 - - + +
155A LEU* 4.2 2.0 - - + -
156A ARG* 3.5 26.5 - - + +
161A LEU* 3.2 46.7 + - + +
162A PRO 3.7 3.1 - - - +
163A TRP* 1.3 107.1 - - + +
165A ARG* 1.3 70.5 + - - +
191A THR* 3.5 29.8 - - + +
192A GLN 3.9 3.1 - - - +
206A VAL* 5.1 3.6 - - + -
210A VAL* 5.3 1.8 - - + -
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Residues in contact with ARG 165 (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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152A GLN* 3.5 17.8 + - - -
156A ARG* 3.4 6.3 - - - +
162A PRO 3.1 25.9 + - - -
163A TRP* 3.3 12.5 + - - +
164A LEU* 1.3 76.2 + - - +
166A PRO* 1.3 79.6 - - + +
167A ASP 3.4 3.2 + - - +
192A GLN* 3.2 41.9 + - + +
193A HIS 3.6 5.6 - - - +
194A ALA* 3.5 37.8 - - - +
195A PRO* 5.4 1.6 - - - +
235A VAL 5.6 0.9 - - - -
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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
----------------------------------------------------------
13A SER* 2.6 30.2 + - - -
14A GLU* 5.4 0.3 - - - +
15A GLY* 3.8 9.5 + - - -
77A ILE 3.7 24.5 - - - +
78A GLY* 3.8 24.7 - - - +
79A TYR* 3.7 26.7 - - + -
152A GLN* 3.9 5.9 - - - +
156A ARG* 3.5 20.3 + - - +
165A ARG* 1.3 98.0 - - + +
167A ASP* 1.3 52.2 + - - +
192A GLN* 3.7 5.8 - - - +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.6 2.7 - - - -
15A GLY 3.6 10.3 - - - -
16A HIS* 3.3 25.8 - - - +
17A PRO* 3.7 7.1 - - - +
79A TYR* 3.6 3.3 + - - +
165A ARG 3.4 0.2 + - - -
166A PRO* 1.3 75.4 - - - +
168A ALA* 1.3 73.6 + - - +
169A LYS* 5.0 1.2 - - - +
191A THR* 3.9 1.4 + - - -
192A GLN* 2.8 50.3 + - + +
234A PHE* 3.8 18.4 - - + -
237A GLY* 3.8 0.3 - - - -
238A GLY* 2.8 29.8 + - - +
242A ASP* 4.5 4.7 - - - +
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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
----------------------------------------------------------
12A VAL* 3.4 4.0 - - - +
13A SER* 2.8 35.3 + - - -
149A VAL* 4.4 4.7 - - + -
152A GLN* 3.8 35.0 - - + +
167A ASP* 1.3 81.3 + - - +
169A LYS* 1.3 67.2 + - - +
189A LEU* 4.8 2.9 - - + -
190A SER 3.1 15.5 - - - +
191A THR* 3.9 4.3 - - - +
234A PHE* 5.0 2.2 - - - -
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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
----------------------------------------------------------
10A GLU* 4.3 6.1 + - - -
11A SER 3.5 6.1 - - - +
12A VAL* 4.2 12.8 - - + -
16A HIS* 4.1 33.5 + - + -
149A VAL* 4.0 4.0 - - - -
167A ASP* 5.0 1.3 - - - +
168A ALA* 1.3 80.4 - - - +
170A SER* 1.3 61.0 + - - +
188A VAL 4.0 0.2 - - - +
189A LEU* 3.3 6.3 - - - +
190A SER* 2.9 40.3 + - - +
234A PHE* 6.0 4.3 - - + -
249A LYS* 5.3 4.3 - - - +
122B ASP* 2.7 42.2 + - - +
123B GLN* 3.7 33.8 + - + +
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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
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10A GLU* 3.2 0.7 - - - -
11A SER 2.9 28.4 + - - -
145A SER* 2.7 33.1 + - - -
148A LEU* 3.9 20.9 - - - -
149A VAL* 3.5 14.7 - - - +
169A LYS* 1.3 75.5 - - - +
171A GLN* 1.3 61.3 + - - +
188A VAL 3.3 10.1 - - - -
189A LEU* 4.6 4.3 - - - -
123B GLN* 2.9 15.4 + - - -
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Residues in contact with GLN 171 (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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8A THR* 3.4 19.1 - - + +
9A SER 3.2 18.2 - - - +
10A GLU* 4.0 6.3 - - + +
145A SER* 4.2 0.2 - - - -
170A SER* 1.3 76.4 - - - +
172A VAL* 1.3 62.0 + - - +
173A THR* 4.8 2.0 + - - -
186A THR 3.7 1.2 - - - +
187A VAL* 3.4 4.2 - - - -
188A VAL* 2.9 52.2 + - + +
123B GLN* 3.7 14.7 + - - +
124B GLY* 2.8 40.2 + - - -
125B LEU* 4.5 0.2 - - - +
303B SER* 4.1 1.4 - - - -
304B TYR 3.1 20.2 + - - -
312B THR* 3.6 17.8 + - - -
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Residues in contact with VAL 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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7A PHE 3.9 1.2 - - - +
8A THR* 3.4 2.9 - - - -
9A SER 3.0 29.8 + - - -
141A PRO* 3.9 10.9 - - + +
144A LEU* 4.1 18.2 - - + -
145A SER* 3.5 26.0 + - - +
148A LEU* 3.6 28.9 - - + -
171A GLN* 1.3 77.2 - - - +
173A THR* 1.3 64.0 + - - +
174A VAL* 3.9 19.6 + - + -
184A ILE* 4.2 19.7 - - + -
186A THR 3.6 2.5 - - - +
187A VAL* 4.5 5.2 - - + -
215A LEU* 5.2 0.7 - - + -
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Residues in contact with THR 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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6A LEU* 4.1 12.3 - - + -
7A PHE 3.5 3.6 - - - +
8A THR* 2.8 28.9 + - - +
171A GLN* 4.8 3.1 + - - +
172A VAL* 1.3 70.8 - - - +
174A VAL* 1.3 62.7 + - - +
184A ILE* 3.8 4.3 - - - +
185A ASP* 2.9 46.8 + - + +
186A THR* 2.9 27.6 + - - +
303B SER* 4.3 3.8 + - - -
312B THR* 4.4 7.5 + - - +
313B SER* 3.9 18.0 - - - -
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Residues in contact with VAL 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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6A LEU* 3.4 3.0 - - - -
7A PHE 2.7 38.3 + - - +
140A LEU* 4.2 11.7 - - + -
141A PRO* 3.8 20.6 - - + -
172A VAL* 3.9 9.8 + - + -
173A THR* 1.3 76.0 - - - +
175A ARG* 1.3 68.2 + - - +
176A TYR* 3.3 38.0 - - + -
181A PRO* 4.3 14.6 - - + -
183A SER 3.8 7.6 - - - +
184A ILE* 3.9 20.9 - - + -
219A LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 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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4A ASP* 2.5 44.7 + - - +
5A TYR 3.3 5.6 - - - +
6A LEU* 3.5 23.3 - - + +
173A THR 4.1 1.2 + - - -
174A VAL* 1.3 71.7 - - - +
176A TYR* 1.3 59.4 + - - +
177A VAL* 4.3 9.5 - - + +
182A HIS* 2.9 49.5 + - - +
183A SER* 3.1 31.7 + - - +
185A ASP* 4.6 7.5 - - + +
223A ASP* 5.1 11.2 + - - -
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Residues in contact with TYR 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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4A ASP* 3.4 5.0 - - - +
5A TYR* 2.7 73.5 + + + -
7A PHE* 3.9 18.4 - + + -
133A GLU* 2.8 42.0 + - - -
139A PRO* 5.2 0.7 - - - +
140A LEU* 4.2 1.2 - - - +
141A PRO* 3.3 21.3 - - + +
174A VAL* 3.3 35.2 - - + -
175A ARG* 1.3 72.3 - - - +
177A VAL* 1.3 63.2 + - - +
178A ASP 4.3 0.2 - - - -
179A GLY 4.1 2.5 - - - -
180A LYS 3.3 26.9 - - - +
181A PRO* 3.6 9.6 - - + -
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Residues in contact with VAL 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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3A ASN 3.3 8.5 - - - +
4A ASP* 3.7 22.0 - - + +
175A ARG* 4.3 11.7 - - - +
176A TYR* 1.3 78.8 - - - +
178A ASP* 1.3 85.4 + - + +
179A GLY 3.2 0.7 - - - -
180A LYS* 2.8 23.4 + - - +
182A HIS* 4.0 32.6 - - + +
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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