Contacts of the strand formed by residues 175 - 181 (chain D) in PDB entry 3E2A
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 SER 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D GLU 2.8 9.9 + - - -
92D HIS* 2.5 38.6 + - - -
93D ILE 3.0 25.6 + - - +
173D LYS* 6.3 0.2 - - - -
174D LEU* 1.3 76.0 - - - +
176D LEU* 1.3 64.5 + - - +
177D HIS* 2.7 20.1 + - - -
194D MET* 4.4 2.5 - - - -
195D ALA 3.2 9.4 - - - -
196D THR* 4.0 15.0 - - - -
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Residues in contact with LEU 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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93D ILE* 3.4 32.3 - - + +
155D VAL* 3.9 21.3 - - + +
158D LEU* 4.1 12.8 - - + -
159D GLY* 3.4 38.1 - - - +
164D VAL* 4.2 6.5 - - + -
168D TRP* 3.8 22.2 - - + -
174D LEU* 4.1 12.3 - - + -
175D SER* 1.3 79.7 - - - +
177D HIS* 1.3 66.4 + - - +
194D MET* 3.2 10.6 - - - +
195D ALA* 2.9 34.3 + - + +
201D LEU* 4.5 0.7 - - + -
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Residues in contact with HIS 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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92D HIS* 3.4 9.8 + + + -
93D ILE 2.8 17.4 + - - +
94D ILE* 3.4 9.1 - - + -
95D ILE* 2.7 32.3 + - - +
155D VAL* 3.6 9.2 - - - +
158D LEU* 5.9 0.3 - - - +
175D SER* 2.7 37.5 + - - -
176D LEU* 1.3 75.8 - - - +
178D GLY* 1.3 54.7 + - - +
179D TRP* 3.6 32.0 + + + +
193D VAL 4.0 3.6 - - - -
194D MET* 3.7 23.9 - - + +
4F ILE* 3.5 32.5 - - + +
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Residues in contact with GLY 178 (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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95D ILE 3.4 2.9 - - - -
151D VAL* 3.3 24.7 - - - -
155D VAL* 3.3 13.5 - - - +
177D HIS* 1.3 74.1 - - - +
179D TRP* 1.3 65.1 + - - -
190D ASP* 3.2 3.5 + - - +
191D GLN* 3.0 27.4 + - - +
192D GLY 4.4 0.3 + - - -
193D VAL* 3.5 8.6 + - - +
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Residues in contact with TRP 179 (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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39D TRP* 4.0 5.6 - + - -
94D ILE* 3.5 40.8 - - + -
95D ILE 2.8 11.6 + - - +
96D CYS* 3.3 3.1 - - - -
97D GLY 2.8 30.0 + - - -
151D VAL* 3.6 5.0 - - - +
177D HIS* 3.6 26.0 + + + +
178D GLY* 1.3 89.1 - - - -
180D VAL* 1.3 59.0 + - - +
181D PHE 4.2 0.4 - - - -
188D LEU* 3.9 29.4 - - + -
189D VAL 3.4 10.1 - - - +
190D ASP* 3.7 24.8 + - + -
191D GLN* 4.4 0.4 - - - -
4F ILE* 3.8 17.5 - - + -
7F LEU* 3.5 34.1 - - + -
8F PHE* 3.4 35.6 - + - -
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Residues in contact with VAL 180 (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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96D CYS* 4.5 1.1 - - - -
97D GLY* 3.4 4.5 - - - -
98D HIS* 4.0 17.0 - - - +
99D THR* 4.3 11.7 - - + -
147D THR* 4.6 6.3 - - + +
148D LYS* 4.2 17.7 - - + +
151D VAL* 3.9 14.6 - - + -
179D TRP* 1.3 77.5 - - - +
181D PHE* 1.3 73.7 + - - +
182D ASP* 3.7 3.6 + - + +
188D LEU* 3.6 1.9 - - - -
189D VAL* 2.7 42.4 + - + +
191D GLN* 3.4 33.7 - - + +
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Residues in contact with PHE 181 (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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47D VAL* 4.0 26.0 - - + -
52D LEU* 3.9 36.3 - - + -
96D CYS* 3.8 15.4 - - - -
97D GLY 2.9 14.3 + - - +
98D HIS* 3.3 22.2 - - + -
99D THR 3.4 6.6 + - - -
180D VAL* 1.3 72.4 - - - +
182D ASP* 1.3 60.5 + - - +
183D VAL* 3.4 35.9 + - + -
186D GLY* 3.5 30.5 - - - -
187D PHE 3.8 10.1 - - - -
188D LEU* 4.2 5.2 - - + -
232D SO4 3.5 26.6 + - - -
14F TRP* 4.2 5.4 - + - -
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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