Contacts of the strand formed by residues 204 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.7 30.5 - - + -
116A ILE* 3.7 34.8 - - + -
119A TYR* 3.4 27.8 - - + +
120A LYS* 4.2 14.6 - - - +
122A LEU* 4.2 6.5 - - + -
161A ILE* 4.4 7.5 - - + +
162A GLN 3.5 16.3 + - - -
197A GLY 3.8 12.6 - - - +
198A LYS* 4.0 14.4 - - + +
202A GLY 3.9 2.6 + - - -
203A GLU* 1.3 79.4 - - - +
205A SER* 1.3 65.7 + - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.8 8.5 - - - -
161A ILE* 5.1 0.4 - - - -
162A GLN* 3.3 29.8 - - - +
164A LEU* 4.2 11.5 - - - +
196A PRO* 3.6 1.9 - - - +
197A GLY 2.6 42.3 + - - +
199A SER* 3.9 5.7 + - - -
203A GLU 3.5 9.3 + - - -
204A LEU* 1.3 77.9 - - - +
206A ILE* 1.3 61.3 + - - +
207A PHE* 3.5 19.5 - - - -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 4.0 22.1 - - + -
133A LEU* 4.8 5.4 - - + +
135A ILE* 3.5 33.7 - - + -
161A ILE* 3.8 14.8 - - + -
162A GLN 3.1 11.5 + - - +
163A VAL* 3.9 15.0 - - + -
164A LEU 3.0 22.0 + - - -
192A ILE* 3.6 23.8 - - + +
194A GLY 4.1 17.7 - - - +
195A PHE 3.8 10.1 - - - +
205A SER* 1.3 74.6 - - - +
207A PHE* 1.3 67.8 + - - +
208A PRO* 3.2 4.2 - - - +
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A HIS* 3.3 35.0 - + - -
164A LEU* 3.2 49.4 - - + +
166A ASN 5.8 0.2 - - - +
169A PHE* 4.3 15.0 - + + -
194A GLY* 3.0 2.7 - - - -
195A PHE* 2.9 77.3 + + + +
197A GLY* 3.6 26.7 - - - -
198A LYS 3.6 11.4 - - - -
199A SER* 4.7 0.7 - - - -
200A LYS* 5.1 2.7 - - - -
205A SER* 3.5 15.7 - - - -
206A ILE* 1.3 74.4 - - - +
208A PRO* 1.3 65.9 - - - +
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Residues in contact with PRO 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.0 17.9 - - + -
164A LEU 3.2 12.1 - - - +
165A ALA* 4.1 11.0 - - + +
166A ASN 5.0 4.2 + - - +
169A PHE* 4.5 9.9 - - - +
170A HIS* 4.6 4.5 - - - +
181A TYR* 3.2 25.9 + - + +
192A ILE* 3.5 19.5 - - + -
193A VAL 3.3 7.2 - - - +
194A GLY* 3.8 2.5 - - - -
206A ILE* 3.2 13.0 - - - +
207A PHE* 1.3 84.6 - - - +
209A LYS* 1.3 61.9 + - - +
210A GLU 3.7 4.7 - - - +
211A THR* 3.5 12.3 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 5.5 3.8 + - - +
132A ILE* 4.2 21.3 - - + +
169A PHE* 3.1 44.2 + - - +
170A HIS* 2.7 28.7 + - - +
171A ASN* 2.7 37.1 + - - +
181A TYR* 4.7 0.2 - - - -
193A VAL* 2.5 23.1 + - + +
194A GLY* 4.0 11.2 - - - -
195A PHE* 4.7 12.1 - - + -
207A PHE 4.6 1.6 - - - +
208A PRO* 1.3 74.4 - - - +
210A GLU* 1.3 55.4 + - + +
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A HIS* 4.2 8.5 - - + -
171A ASN* 5.1 5.0 + - + +
174A LYS* 3.2 53.2 - - + +
181A TYR* 4.0 1.6 - - - -
192A ILE* 3.7 1.6 - - - -
193A VAL* 3.0 60.1 + - + +
208A PRO* 3.3 2.2 - - - +
209A LYS* 1.3 82.1 - - + +
211A THR* 1.3 66.1 + - - +
212A ILE* 4.3 18.9 + - + +
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Residues in contact with THR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 6.1 0.9 - - + -
152A PHE* 6.2 0.4 - - + -
163A VAL* 5.6 0.8 - - + +
170A HIS* 5.2 0.8 - - - -
180A CYS* 5.1 15.2 - - - +
181A TYR* 2.5 43.4 + - + -
184A ILE* 4.0 22.0 - - + +
190A VAL* 4.0 20.9 - - + -
191A GLY 3.6 10.8 - - - +
192A ILE* 4.0 9.6 - - + +
208A PRO* 3.5 9.7 - - - +
210A GLU* 1.3 76.4 + - - +
212A ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASN 6.0 1.1 - - - +
103A PRO* 5.1 10.8 - - + -
106A PHE* 3.8 28.9 - - + -
190A VAL* 3.3 8.8 - - - +
191A GLY 3.0 37.1 + - - +
193A VAL* 5.0 3.4 - - + -
210A GLU* 4.3 24.7 - - + +
211A THR* 1.3 78.6 - - - +
213A LEU* 1.3 67.6 + - - +
214A LEU* 3.7 4.7 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 4.2 21.3 - - - +
90A PHE* 4.4 16.6 - - + -
94A GLN* 5.5 2.0 - - - +
100A ASN 4.4 0.9 - - - +
101A PRO* 3.1 49.1 - - + +
103A PRO* 3.1 14.2 - - - +
183A LYS* 4.7 12.1 - - + +
184A ILE* 5.6 4.5 - - + -
188A ASP* 4.5 10.5 - - + +
189A ILE 4.1 3.4 - - - +
190A VAL* 4.1 7.2 - - + -
211A THR 4.3 0.2 + - - -
212A ILE* 1.3 77.1 - - - +
214A LEU* 1.3 59.2 + - - +
215A SER 3.4 28.5 - - - +
216A ALA* 3.5 10.5 - - + +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PRO 3.4 3.1 - - - +
102A TYR* 3.6 7.8 - - - -
103A PRO* 3.3 36.5 - - + +
105A LYS 5.4 0.2 - - - +
106A PHE* 3.6 31.4 - - + +
136A THR* 3.6 12.8 - - + -
189A ILE* 2.8 17.5 + - + +
190A VAL 3.7 2.5 - - - -
191A GLY* 3.3 26.7 - - - +
212A ILE* 3.5 5.4 + - + +
213A LEU* 1.3 73.0 - - - +
215A SER* 1.3 59.3 + - - +
351B TYR* 3.4 33.0 - - + -
509B ASN* 4.6 1.0 + - - -
549B PRO* 3.8 25.8 - - + +
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PRO 4.1 2.0 - - - -
102A TYR* 3.4 16.5 - - - -
188A ASP 3.8 0.5 - - - -
189A ILE* 2.9 39.2 + - - +
213A LEU* 3.4 8.1 - - - +
214A LEU* 1.3 79.3 - - - +
216A ALA* 1.3 61.3 + - - +
509B ASN* 4.8 0.4 - - - -
546B GLY* 3.5 3.1 - - - -
547B LEU 2.8 47.0 + - - -
548B PRO* 4.1 6.7 - - - -
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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