Contacts of the strand formed by residues 204 - 215 (chain C) in PDB entry 4YCV
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 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.8 24.9 - - + +
116C ILE* 3.8 39.9 - - + +
119C TYR* 3.8 22.2 - - + +
120C LYS* 5.1 5.4 - - - +
122C LEU* 3.8 17.0 - - + -
161C ILE* 4.6 9.7 - - + -
162C GLN* 3.4 17.5 + - - +
197C GLY 4.0 14.1 - - - +
198C LYS* 4.0 6.2 - - + +
203C GLU* 1.3 71.3 - - - +
205C SER* 1.3 79.9 + - - +
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Residues in contact with SER 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.8 8.5 - - - -
161C ILE* 5.0 2.2 - - - +
162C GLN* 3.2 41.7 + - - +
164C LEU* 4.3 18.1 - - - +
196C PRO* 3.7 2.9 - - - +
197C GLY 2.7 40.0 + - - +
198C LYS* 4.9 0.4 - - - -
199C SER 5.0 1.2 + - - -
203C GLU 3.3 4.3 + - - -
204C LEU* 1.3 88.7 + - - +
206C ILE* 1.3 61.1 + - - +
207C PHE* 4.4 5.8 - - - -
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 4.0 15.9 - - + -
133C LEU* 5.0 4.5 - - + +
135C ILE* 3.9 13.5 - - + -
154C LEU* 5.2 0.2 - - + -
161C ILE* 3.9 20.4 - - + -
162C GLN 3.1 13.7 + - - +
163C VAL* 3.6 23.3 - - + -
164C LEU 3.0 22.1 + - - -
192C ILE* 3.8 26.7 - - + -
194C GLY* 3.7 9.0 - - - +
195C PHE 3.6 33.2 - - - +
196C PRO* 4.0 2.7 - - + -
205C SER* 1.3 74.9 - - - +
207C PHE* 1.3 60.7 + - - +
208C PRO* 3.1 5.7 - - - +
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Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLU 4.9 0.9 - - - -
127C HIS* 4.5 17.9 - + - -
164C LEU* 3.1 44.2 - - + +
166C ASN 5.8 0.4 - - - +
169C PHE* 4.5 15.0 - + + -
194C GLY* 3.1 1.4 - - - -
195C PHE* 2.9 79.1 + + + +
197C GLY* 3.2 40.8 - - - -
198C LYS 4.3 13.0 - - - -
199C SER* 4.3 7.2 - - - -
205C SER* 4.0 5.6 - - - -
206C ILE* 1.3 74.3 - - - +
208C PRO* 1.3 67.8 - - - +
209C LYS 3.5 0.5 + - - -
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Residues in contact with PRO 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 4.1 11.9 - - + -
164C LEU 3.1 17.0 - - - +
165C ALA* 3.7 14.5 - - + +
166C ASN 4.8 3.8 + - - +
169C PHE* 4.1 11.3 - - - +
170C HIS* 4.2 8.3 + - - +
181C TYR* 3.4 18.5 + - + +
192C ILE* 3.6 16.2 - - + -
193C VAL 3.5 5.6 - - - +
194C GLY* 3.7 2.5 - - - -
195C PHE* 5.7 0.2 - - - -
206C ILE 3.1 10.1 - - - +
207C PHE* 1.3 84.0 - - - +
209C LYS* 1.3 61.5 + - - +
210C GLU 3.7 4.3 - - - +
211C THR* 3.1 23.3 - - - +
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Residues in contact with LYS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 5.6 7.9 - - + -
169C PHE* 3.6 16.8 - - - +
170C HIS* 3.1 10.0 - - - -
171C ASN* 2.6 37.9 + - + +
193C VAL* 2.7 20.1 + - + +
194C GLY* 3.7 3.1 - - - -
195C PHE* 5.5 4.5 - - + -
207C PHE 3.5 3.6 + - - -
208C PRO* 1.3 72.8 - - - +
210C GLU* 1.3 62.0 + - + +
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Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C HIS* 4.6 4.7 - - + +
171C ASN* 4.7 16.8 + - + +
174C LYS* 4.6 23.6 - - + +
181C TYR* 4.4 3.8 - - - -
192C ILE* 3.8 0.2 - - - -
193C VAL* 3.0 61.9 + - + +
208C PRO* 3.3 3.6 - - - +
209C LYS* 1.3 82.4 - - + +
211C THR* 1.3 66.7 + - - +
212C ILE* 5.6 8.6 - - + +
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Residues in contact with THR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 5.5 1.0 - - + +
180C CYS* 5.5 8.5 - - - +
181C TYR* 2.9 33.3 + - + -
184C ILE* 4.1 21.5 - - + -
190C VAL* 4.2 14.4 - - + -
191C GLY 3.8 11.4 - - - +
192C ILE* 3.8 15.3 - - + +
208C PRO* 3.1 19.2 - - - +
210C GLU* 1.3 73.4 + - - +
212C ILE* 1.3 64.8 - - - +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASN 5.6 2.0 - - - +
103C PRO* 4.5 16.4 - - + -
106C PHE* 4.1 25.1 - - + -
190C VAL* 3.6 4.2 - - - +
191C GLY 2.9 35.6 + - - +
193C VAL* 6.3 1.1 - - + -
210C GLU* 5.6 7.9 - - + +
211C THR* 1.3 75.5 - - - +
213C LEU* 1.3 70.0 + - + +
214C LEU* 3.8 4.9 + - + -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 4.7 13.9 - - + -
94C GLN* 4.9 6.3 - - - +
101C PRO* 3.6 37.5 - - + +
103C PRO* 3.1 21.8 - - - +
180C CYS 6.0 0.4 - - - +
183C LYS* 4.7 24.0 - - + +
184C ILE* 5.6 7.2 - - + +
188C ASP* 5.1 9.4 - - - +
189C ILE 3.7 10.8 - - - +
190C VAL* 4.0 12.6 - - + +
212C ILE* 1.3 77.3 - - + +
214C LEU* 1.3 61.0 + - - +
215C SER 4.8 3.8 - - - +
216C ALA* 4.7 14.8 - - + -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO 4.4 1.1 - - - -
102C TYR* 3.5 11.6 - - - -
103C PRO* 3.2 44.6 - - + +
106C PHE* 3.4 43.3 - - + +
136C THR* 3.8 23.1 - - + -
189C ILE* 2.8 21.9 + - + +
190C VAL 4.3 1.6 - - - +
191C GLY 4.2 10.8 - - - +
212C ILE* 3.8 7.1 + - + +
213C LEU* 1.3 74.3 - - - +
215C SER* 1.3 60.1 + - - +
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Residues in contact with SER 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PRO 4.5 0.9 - - - -
102C TYR* 3.6 19.7 - - - -
188C ASP* 3.8 2.3 - - - -
189C ILE* 2.8 54.8 + - - +
213C LEU* 3.6 4.9 - - - +
214C LEU* 1.3 80.9 - - - +
216C ALA* 1.3 64.4 + - - +
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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