Contacts of the strand formed by residues 164 - 177 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D GLN* 3.2 37.9 - - + +
155D LEU* 4.0 4.7 - - + -
156D ARG* 3.6 33.5 - - + +
161D LEU* 3.2 40.7 + - + +
162D PRO 3.3 6.6 - - - +
163D TRP* 1.3 93.1 - - + +
165D ARG* 1.3 63.1 + - - +
191D THR* 3.2 38.6 - - + +
192D GLN 3.9 1.6 - - - +
206D VAL* 5.0 3.4 - - + -
210D VAL* 5.2 1.6 - - + -
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D GLN* 3.3 18.9 + - - -
156D ARG* 3.4 7.0 - - - +
163D TRP 3.6 1.8 + - - -
164D LEU* 1.3 74.6 - - - +
166D PRO* 1.3 78.2 - - + +
167D ASP 3.4 5.6 + - - +
192D GLN* 2.9 35.5 + - + +
193D HIS 3.4 12.3 + - - -
194D ALA* 3.4 34.8 - - - +
195D PRO* 3.9 7.8 - - - +
235D VAL* 3.0 35.9 + - - +
236D ILE* 5.1 2.4 - - - +
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Residues in contact with PRO 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D SER* 2.7 28.6 + - - -
14D GLU* 5.2 0.3 - - - +
15D GLY* 3.7 9.6 + - - -
77D ILE 3.8 16.6 - - - +
78D GLY 3.9 26.5 - - - +
79D TYR* 3.6 32.8 - - + +
152D GLN* 4.1 5.5 - - - +
153D ALA* 6.0 0.2 - - - +
156D ARG* 3.5 20.3 + - - +
165D ARG* 1.3 98.2 - - + +
167D ASP* 1.3 50.7 + - - +
192D GLN* 3.5 7.0 - - - +
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Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D SER* 3.5 2.7 - - - -
15D GLY 3.8 12.1 - - - -
16D HIS* 3.3 26.4 - - - +
17D PRO* 3.7 9.7 - - - +
79D TYR* 3.7 7.4 - - - +
165D ARG 3.7 2.3 - - - +
166D PRO* 1.3 75.1 - - - +
168D ALA* 1.3 73.5 + - - +
169D LYS* 4.6 1.4 - - - +
192D GLN* 2.9 52.7 + - + +
234D PHE* 3.8 20.0 - - + -
237D GLY* 3.9 1.0 - - - -
238D GLY 3.0 21.0 + - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.4 1.0 - - - +
13D SER* 2.8 34.3 + - - -
149D VAL* 4.2 5.6 - - + -
152D GLN* 3.7 35.4 - - + +
167D ASP* 1.3 82.0 + - - +
169D LYS* 1.3 70.7 + - - +
189D LEU* 5.3 2.2 - - + -
190D SER 3.1 14.1 - - - +
191D THR* 3.9 4.3 - - - +
192D GLN 4.7 0.2 - - - +
234D PHE* 4.7 2.2 - - - -
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASP* 3.3 33.7 + - - +
123C GLN* 3.8 34.6 + - - +
10D GLU* 5.4 5.3 + - - -
11D SER 3.5 5.6 - - - +
12D VAL* 3.8 24.0 - - + +
16D HIS* 3.8 26.9 + - + +
149D VAL* 3.9 4.0 - - - -
167D ASP* 4.6 2.5 - - - +
168D ALA* 1.3 80.6 - - - +
170D SER* 1.3 59.4 + - - +
189D LEU* 3.5 4.3 - - - +
190D SER* 2.8 41.8 + - - +
234D PHE* 5.9 5.2 - - + -
249D LYS* 5.2 4.8 - - - +
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Residues in contact with SER 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLN* 3.0 13.5 + - - -
10D GLU* 3.3 0.5 - - - -
11D SER* 2.9 30.9 + - - -
145D SER* 2.7 33.5 + - - -
148D LEU* 4.1 19.5 - - - -
149D VAL* 3.6 10.0 - - - +
169D LYS* 1.3 74.8 - - - +
171D GLN* 1.3 59.9 + - - +
188D VAL 3.3 10.3 - - - -
189D LEU* 5.1 3.4 - - - -
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 3.4 16.3 + - - +
124C GLY* 3.0 34.5 + - - +
125C LEU* 5.7 0.2 - - - -
303C SER* 3.1 16.6 + - - -
304C TYR 2.9 19.1 + - - +
305C ALA 4.3 0.2 - - - +
312C THR* 3.1 14.3 + - - +
8D THR* 3.4 16.2 - - + +
9D SER 3.2 20.0 - - - +
10D GLU* 4.0 5.3 - - + +
145D SER* 4.2 0.2 - - - -
170D SER* 1.3 75.0 - - - +
172D VAL* 1.3 62.0 + - - +
173D THR* 4.5 2.5 + - - +
186D THR* 3.8 1.2 - - - +
187D VAL* 3.4 3.8 - - - -
188D VAL* 2.7 52.9 + - + +
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Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE 3.8 1.4 - - - +
8D THR* 3.3 2.6 - - - -
9D SER 3.0 31.2 + - - -
141D PRO* 3.9 10.5 - - - +
144D LEU* 4.1 17.9 - - + -
145D SER* 3.4 25.5 + - - +
148D LEU* 3.8 28.0 - - + -
171D GLN* 1.3 76.1 - - - +
173D THR* 1.3 64.8 + - - +
174D VAL* 3.9 23.0 + - + -
184D ILE* 4.3 13.0 - - + -
186D THR 3.5 6.7 - - - +
187D VAL* 4.6 5.6 - - + -
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Residues in contact with THR 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 4.0 13.8 + - - +
313C SER* 2.8 24.3 + - - +
6D LEU* 4.0 16.4 - - + -
7D PHE 3.4 5.2 - - - +
8D THR* 2.5 22.4 + - - +
171D GLN* 4.2 2.5 + - - +
172D VAL* 1.3 72.9 - - - +
174D VAL* 1.3 61.6 + - - +
184D ILE* 3.8 3.5 - - - +
185D ASP* 2.9 41.2 + - + +
186D THR* 2.9 25.7 + - - +
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.4 4.5 - - - -
7D PHE 2.8 36.5 + - - +
140D LEU* 4.1 30.1 - - + -
141D PRO* 4.1 13.7 - - + -
144D LEU* 5.1 0.2 - - + -
172D VAL* 3.9 19.3 - - + -
173D THR* 1.3 77.0 - - - +
175D ARG* 1.3 74.3 + - - +
176D TYR* 3.6 29.0 - - + -
181D PRO* 4.4 6.5 - - + -
183D SER 3.7 11.2 - - - +
184D ILE* 4.7 7.6 - - + -
219D LEU* 5.7 0.4 - - + -
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Residues in contact with ARG 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR 3.5 9.7 - - - +
6D LEU* 3.6 23.2 - - + +
173D THR 4.3 0.6 + - - -
174D VAL* 1.3 76.8 - - - +
176D TYR* 1.3 66.8 + - - +
177D VAL* 5.7 5.4 - - - +
182D HIS* 2.9 61.8 + - - +
183D SER* 2.8 26.8 + - - +
185D ASP* 4.6 3.5 - - + +
223D ASP* 5.2 8.2 + - - -
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 2.8 78.1 + + + +
7D PHE* 3.8 20.7 - + + -
133D GLU* 2.6 40.5 + - - -
139D PRO* 5.0 0.9 - - - +
140D LEU* 4.1 0.9 - - - +
141D PRO* 3.2 20.8 - - + +
174D VAL* 3.6 30.1 - - + -
175D ARG* 1.3 77.0 + - - +
177D VAL* 1.3 59.7 + - - +
178D ASP 4.4 0.3 + - - -
179D GLY 3.7 14.6 - - - -
180D LYS 3.3 20.0 - - - +
181D PRO* 3.7 11.4 - - + -
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 4.1 7.9 + - - +
176D TYR* 1.3 73.6 - - - +
178D ASP* 1.3 79.6 + - + +
179D GLY 3.1 1.6 - - - -
180D LYS* 2.9 22.8 + - + +
181D PRO 5.1 0.7 - - - +
182D HIS* 3.4 40.2 - - + +
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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