Contacts of the helix formed by residues 187 - 197 (chain I) in PDB entry 3J7Y
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 187 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178I GLY* 4.4 5.8 - - - -
185I ILE 3.7 3.0 + - - -
186I LEU* 1.3 80.9 - - - +
188I ARG* 1.3 67.0 + - - +
189I GLN* 3.5 6.6 + - - +
190I GLY* 3.8 14.0 - - - -
191I PHE* 3.0 27.0 + - - +
21k CYS* 6.0 0.2 - - - -
22k PRO* 4.2 16.4 - - - +
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Residues in contact with ARG 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLN* 4.5 9.4 - - - +
174I LEU* 3.2 45.0 + - - +
176I LEU* 3.4 26.2 + - + +
177I LEU* 4.8 10.0 - - + +
178I GLY* 4.7 4.9 - - - +
187I SER* 1.3 78.8 + - - +
189I GLN* 1.3 57.4 + - - +
191I PHE* 3.2 16.0 + - - +
192I ILE* 3.2 13.3 + - - +
20k PHE* 3.4 47.8 + - - +
21k CYS* 4.6 2.7 - - - +
22k PRO* 4.1 33.9 - - + +
34k LEU* 5.3 2.4 - - - +
53k ALA* 4.8 4.4 - - - +
54k ASP 4.5 3.6 + - - -
55k VAL* 3.3 28.2 - - + +
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Residues in contact with GLN 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I SER* 3.5 5.2 + - - +
188I ARG* 1.3 76.3 - - - +
190I GLY* 1.3 62.9 + - - +
191I PHE 3.2 0.7 - - - -
192I ILE* 3.0 39.0 - - + +
193I ASN* 3.2 9.7 + - - +
21k CYS* 4.6 12.3 - - - -
55k VAL* 3.5 39.3 + - - +
56k ARG* 5.9 0.4 - - - +
57k HIS* 6.2 1.2 - - - -
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Residues in contact with GLY 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I LEU* 3.5 24.3 - - - +
187I SER* 3.8 14.2 + - - -
188I ARG 3.3 0.4 - - - -
189I GLN* 1.3 77.3 - - - +
191I PHE* 1.3 57.8 + - - +
193I ASN* 3.2 8.9 + - - +
194I TYR* 2.9 25.6 + - - +
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Residues in contact with PHE 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I MET* 4.9 4.0 - - + -
97I ALA* 3.7 26.5 - - + -
98I VAL 4.7 2.9 - - - -
161I VAL* 3.7 28.0 - - + -
165I VAL* 5.1 0.7 - - + -
176I LEU* 3.5 59.5 - - + -
179I GLY* 3.7 25.8 - - - -
186I LEU* 3.3 27.1 - - + +
187I SER 3.0 14.2 + - - +
188I ARG* 3.2 11.2 + - - +
190I GLY* 1.3 77.0 - - - +
192I ILE* 1.3 53.1 + - - +
194I TYR* 3.2 7.7 + + - +
195I SER* 2.7 40.5 + - - -
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Residues in contact with ILE 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I VAL* 5.9 1.8 - - + -
169I ARG* 3.8 29.3 + - - +
174I LEU* 5.9 7.6 - - + -
188I ARG 3.2 5.1 + - - +
189I GLN* 3.0 50.0 - - + +
191I PHE* 1.3 78.6 - - - +
193I ASN* 1.3 58.0 + - - +
195I SER* 3.2 7.8 + - - -
196I LYS* 2.9 28.9 + - + +
55k VAL* 6.0 4.9 - - + -
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Residues in contact with ASN 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I GLN 3.2 13.3 + - - +
190I GLY* 3.2 12.4 + - - +
192I ILE* 1.3 79.0 - - + +
194I TYR* 1.3 62.9 + - - +
196I LYS* 3.2 20.6 + - - +
197I LEU* 3.0 35.8 + - - +
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Residues in contact with TYR 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I ARG* 5.8 0.9 + - - -
95I MET* 3.3 35.3 - - + +
159I PRO* 3.6 18.5 - - + +
161I VAL* 3.5 23.8 - - + -
162I LYS* 5.7 1.7 - - + +
181I ILE* 3.9 20.9 - - + +
186I LEU* 4.4 9.4 - - + -
190I GLY 2.9 13.1 + - - +
191I PHE* 3.4 17.9 - + - +
193I ASN* 1.3 77.5 - - - +
195I SER* 1.3 62.9 + - - +
197I LEU* 3.1 41.9 + - + +
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Residues in contact with SER 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I VAL* 5.4 0.3 - - - +
162I LYS* 2.8 48.9 + - - +
165I VAL* 3.4 41.0 - - - +
169I ARG* 4.5 7.2 - - - -
191I PHE* 2.7 22.8 + - - -
192I ILE* 3.2 9.1 + - - -
194I TYR* 1.3 78.7 - - - +
196I LYS* 1.3 58.4 + - - +
197I LEU 3.3 7.1 - - - +
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Residues in contact with LYS 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I LYS* 4.3 7.9 + - - +
169I ARG* 5.6 1.3 - - - +
192I ILE* 2.9 13.9 + - + +
193I ASN* 3.3 22.7 + - - +
195I SER* 1.3 78.6 - - - +
197I LEU* 1.3 65.4 + - + +
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Residues in contact with LEU 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I LYS* 4.4 9.7 - - - +
193I ASN* 3.0 31.6 + - - +
194I TYR* 3.1 38.2 + - + +
195I SER 3.3 7.6 - - - +
196I LYS* 1.3 84.0 - - - +
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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