Contacts of the helix formed by residues 187 - 197 (chain D) in PDB entry 2W7U
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 THR 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D GLY* 3.6 28.7 - - - +
141D THR* 4.6 4.1 - - - -
185D TYR* 3.2 13.6 + - + +
186D PHE* 1.3 76.0 - - - +
188D PRO* 1.3 74.8 - - + +
189D GLN* 3.7 17.4 + - - +
190D LEU* 3.0 25.8 + - - +
191D LYS* 3.0 22.9 + - - -
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Residues in contact with PRO 188 (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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186D PHE 4.6 1.1 - - - +
187D THR* 1.3 89.2 - - + +
189D GLN* 1.3 71.9 + - - +
191D LYS* 3.8 18.4 - - + +
192D GLU* 3.0 28.1 + - - +
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Residues in contact with GLN 189 (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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177C GLU* 5.5 6.5 - - - +
73D TYR* 5.3 6.9 - - - +
187D THR* 3.1 20.9 + - - +
188D PRO* 1.3 89.6 - - - +
190D LEU* 1.3 65.9 + - + +
192D GLU* 3.6 11.7 + - - +
193D PHE* 3.4 18.7 + - - +
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Residues in contact with LEU 190 (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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73D TYR* 3.6 39.9 - - + +
77D GLU* 4.6 8.3 - - + +
79D LEU* 3.9 15.9 - - + -
141D THR* 3.3 26.0 - - - +
184D VAL* 4.0 14.6 - - + -
185D TYR 3.4 19.1 - - - +
186D PHE* 4.2 12.3 - - + -
187D THR* 3.0 20.0 + - - +
189D GLN* 1.3 77.4 - - + +
191D LYS* 1.3 58.7 + - - +
193D PHE* 3.3 7.3 + - - +
194D ILE* 3.1 32.1 + - - +
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Residues in contact with LYS 191 (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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103D PHE* 3.6 46.5 - - + +
104D ALA* 2.9 27.1 + - - +
105D ASP* 4.2 10.1 + - - +
106D GLY* 5.1 2.2 - - - +
165D LEU 5.5 0.8 + - - -
186D PHE* 3.4 33.6 + - + +
187D THR 3.0 18.3 + - - +
188D PRO* 3.8 14.2 - - + +
189D GLN 3.3 0.2 - - - -
190D LEU* 1.3 76.0 - - - +
192D GLU* 1.3 60.5 + - - +
194D ILE* 3.4 8.0 + - - +
195D GLN* 2.9 33.7 + - - +
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Residues in contact with GLU 192 (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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2C LYS* 5.3 9.5 - - - +
188D PRO 3.0 16.8 + - - +
189D GLN* 3.8 10.9 - - - +
190D LEU 3.3 0.2 - - - -
191D LYS* 1.3 75.1 - - - +
193D PHE* 1.3 59.2 + - - +
195D GLN* 3.8 5.6 - - + -
196D ASN* 3.0 53.9 + - - +
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Residues in contact with PHE 193 (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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71D VAL* 3.8 18.6 - - + -
72D GLU 3.6 21.5 - - - -
73D TYR* 3.6 43.1 - + + -
74D PRO* 3.9 17.3 - - + -
79D LEU* 4.2 13.9 - - + -
81D ILE* 3.6 22.9 - - + -
189D GLN 3.4 10.0 + - - +
190D LEU 3.3 8.7 + - - +
191D LYS 3.3 0.4 - - - -
192D GLU* 1.3 78.3 - - - +
194D ILE* 1.3 64.5 + - - +
196D ASN* 3.6 3.4 + - - +
197D ASN* 2.8 46.2 + - - +
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Residues in contact with ILE 194 (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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29D VAL* 3.8 26.9 - - + -
35D VAL* 4.2 12.3 - - + -
79D LEU* 4.5 6.3 - - + -
81D ILE* 3.9 22.2 - - + +
103D PHE* 3.8 34.5 - - + -
186D PHE* 4.0 30.1 - - + -
190D LEU 3.1 21.4 + - - +
191D LYS* 3.7 6.7 - - - +
193D PHE* 1.3 79.7 - - + +
195D GLN* 1.3 61.1 - - - +
197D ASN* 3.2 10.7 + - - +
198D ILE* 3.1 21.0 + - + +
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Residues in contact with GLN 195 (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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29D VAL 5.6 0.8 + - - -
103D PHE* 3.9 23.2 - - - -
191D LYS* 2.9 17.3 + - - +
192D GLU* 3.8 7.2 - - - +
194D ILE* 1.3 75.8 - - - +
196D ASN* 1.3 67.4 + - - +
197D ASN 3.4 0.5 + - - -
198D ILE* 3.5 40.0 + - - +
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Residues in contact with ASN 196 (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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192D GLU* 3.0 37.5 + - - +
193D PHE* 4.0 6.4 - - - +
194D ILE 3.3 0.2 - - - -
195D GLN* 1.3 82.2 + - - +
197D ASN* 1.3 62.8 + - - +
198D ILE 3.4 5.5 + - - +
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Residues in contact with ASN 197 (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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33D THR* 3.7 7.3 - - - +
71D VAL* 3.7 26.6 - - - +
81D ILE* 3.9 17.4 - - + +
83D HIS* 2.8 33.2 + - - +
193D PHE* 2.8 49.3 + - - +
194D ILE 3.2 8.9 + - - +
196D ASN* 1.3 84.1 - - - +
198D ILE* 1.3 54.3 + - - +
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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