Contacts of the helix formed by residues 187 - 197 (chain B) in PDB entry 3H1I
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B VAL* 5.2 3.1 - - - -
185B LYS 3.9 9.6 - - - +
186B ILE* 1.3 81.1 - - - +
188B SER* 1.3 62.5 + - - +
189B GLU* 2.9 22.8 + - - +
190B GLN* 2.8 36.5 + - + +
191B LEU* 3.5 24.9 + - - +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 3.6 21.8 + - - -
134B PRO* 3.5 33.1 + - - +
137B VAL* 4.5 7.9 - - - +
187B THR* 1.3 74.4 - - - +
189B GLU* 1.3 65.1 + - - +
191B LEU* 3.9 11.3 - - - +
192B HIS* 3.1 33.1 + - - -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B THR* 2.9 17.3 + - - +
188B SER* 1.3 84.2 + - - +
190B GLN* 1.3 56.3 + - + +
191B LEU 2.4 17.6 + - - -
192B HIS* 2.4 24.9 + - - +
193B HIS* 2.8 36.0 + - + +
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 2.9 27.7 + - - +
62B ASN* 3.4 24.4 + - + +
65B THR* 3.4 8.7 + - - +
182B ARG* 2.4 29.7 + - - +
185B LYS 4.1 1.6 - - - +
186B ILE* 3.5 16.7 - - + +
187B THR* 2.8 34.8 + - + +
189B GLU* 1.3 72.9 - - + +
191B LEU* 1.3 56.0 + - - +
193B HIS* 4.7 6.6 - - - +
194B PHE* 3.0 26.8 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 3.4 30.3 - - - +
68B LEU* 4.1 16.6 - - + -
69B LEU* 3.9 21.9 - - + +
72B ALA* 4.8 9.2 - - + -
132B PHE* 3.1 43.3 - - + -
137B VAL* 4.2 21.8 - - + -
186B ILE* 4.5 0.7 - - + -
187B THR 3.5 17.4 + - - +
188B SER* 3.9 1.8 - - - +
189B GLU 2.4 13.3 + - - -
190B GLN* 1.3 68.7 - - - +
192B HIS* 1.3 67.5 - - - +
194B PHE* 2.7 17.2 + - - +
195B VAL* 3.1 11.3 + - - +
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 5.8 2.6 + - - -
130B PRO* 3.7 23.3 + - + -
131B GLU* 3.8 24.1 - - - -
132B PHE* 3.6 13.1 - + + +
188B SER* 3.1 20.7 + - - +
189B GLU* 2.4 19.9 + - - +
191B LEU* 1.3 70.8 - - - +
193B HIS* 1.3 60.1 + - + +
195B VAL* 2.7 29.4 + - + +
196B GLN* 3.1 34.8 + - + +
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Residues in contact with HIS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU* 2.8 42.8 + - + +
190B GLN* 4.7 5.2 - - - +
192B HIS* 1.3 78.6 - - + +
194B PHE* 1.3 62.2 + - - +
196B GLN* 3.3 21.8 + - - +
197B ASN* 3.0 44.1 + - - +
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 4.2 17.3 - - + -
54B GLY 3.2 32.3 - - - -
57B TYR* 4.2 26.0 - - + -
58B GLU* 4.5 3.1 - - + -
62B ASN* 3.8 18.8 - - - +
65B THR* 3.9 15.0 - - + +
66B ALA* 4.4 12.1 - - + -
69B LEU* 3.9 27.1 - - + -
105B MET* 4.8 1.6 - - - -
190B GLN 3.0 20.7 + - - +
191B LEU* 2.7 14.0 + - + +
193B HIS* 1.3 72.8 - - - +
195B VAL* 1.3 57.8 + - - +
197B ASN* 5.0 0.2 - - - -
198B ASN* 2.9 34.4 + - - +
199B PHE* 4.4 1.2 - + - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.1 31.4 - - + -
127B THR 4.6 6.5 - - - +
128B THR* 5.8 1.6 - - - -
130B PRO* 4.7 16.4 - - + -
132B PHE* 4.4 10.3 - - + -
191B LEU 3.1 8.5 + - - +
192B HIS* 2.7 17.8 + - + +
194B PHE* 1.3 73.0 - - - +
196B GLN* 1.3 65.7 + - + +
197B ASN 3.1 1.6 - - - -
199B PHE* 2.7 61.8 + - + +
226B ILE* 5.9 2.9 - - + -
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B HIS* 3.1 28.8 + - + +
193B HIS* 3.3 33.1 + - - +
195B VAL* 1.3 81.5 - - + +
197B ASN* 1.3 64.2 + - - +
200B THR* 3.6 14.7 - - - +
226B ILE* 4.5 17.8 - - + +
231B GLY* 5.8 0.2 - - - -
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Residues in contact with ASN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B HIS* 3.0 36.5 + - - +
195B VAL 3.1 1.0 - - - -
196B GLN* 1.3 83.8 - - - +
198B ASN* 1.3 69.4 + - - +
200B THR* 4.1 4.7 - - - -
230B ALA 3.6 7.3 - - - +
231B GLY* 4.1 9.3 - - - -
232B THR* 3.5 41.3 + - - +
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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