Contacts of the strand formed by residues 149 - 156 (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 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C ALA 4.1 4.0 - - - +
146C GLY* 3.5 20.8 + - - -
147C GLN 3.4 1.8 + - - -
148C LYS* 1.3 95.1 - - + +
150C ARG* 1.3 69.2 + - - +
151C PHE* 5.0 19.3 - - + -
164C LEU* 4.7 8.3 - - + -
165C ALA 3.4 3.8 - - - +
166C ASN* 3.3 48.0 - - + +
177C PHE* 4.7 0.4 - - - -
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Residues in contact with ARG 150 (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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143C SER 5.1 2.9 + - - +
144C ALA 4.7 4.2 - - - -
145C SER* 2.5 43.6 + - - +
146C GLY* 3.8 11.4 - - - -
147C GLN 4.7 2.0 - - - +
149C LEU* 1.3 80.8 - - - +
151C PHE* 1.3 64.1 + - - +
152C PHE* 3.6 25.9 - - + -
163C VAL 3.5 4.0 - - - +
164C LEU* 3.8 1.2 - - - +
165C ALA* 2.9 45.7 + - + +
177C PHE* 3.8 22.0 - - + -
178C ALA* 4.0 19.1 - - - +
181C TYR* 4.2 21.7 + - + +
182C ASP* 2.4 36.5 + - - +
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Residues in contact with PHE 151 (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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141C ARG* 4.1 14.4 - - - +
143C SER* 3.0 49.2 + - - +
144C ALA 4.8 1.8 + - - -
149C LEU* 5.0 16.8 - - + -
150C ARG* 1.3 79.5 - - - +
152C PHE* 1.3 69.9 + - - +
162C GLN* 4.0 20.2 - - - +
163C VAL 3.6 2.5 - - - -
164C LEU* 3.7 31.4 - - + -
199C SER* 6.1 0.4 - - - -
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Residues in contact with PHE 152 (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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139C ILE* 3.9 28.5 - - + -
141C ARG* 3.3 10.9 + - - +
142C VAL* 3.3 32.5 - - + +
143C SER 4.7 1.1 - - - +
150C ARG* 3.6 37.2 - - + -
151C PHE* 1.3 77.0 - - - +
153C ASP* 1.3 70.1 + - - +
162C GLN* 3.6 5.0 - - - +
163C VAL* 2.8 51.7 + - + +
165C ALA* 5.3 0.2 - - + -
181C TYR* 3.9 29.2 - + - -
184C ILE* 3.9 31.4 - - + -
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Residues in contact with ASP 153 (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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138C ARG 3.5 0.2 - - - +
139C ILE* 3.4 6.0 - - - -
140C MET* 2.9 30.5 + - + -
141C ARG* 2.6 65.7 + - + +
152C PHE* 1.3 80.1 - - - +
154C LEU* 1.3 60.4 + - - +
155C VAL* 3.8 6.1 + - + +
160C LYS* 5.3 7.9 - - + -
161C ILE 3.9 2.6 - - - +
162C GLN* 3.4 18.8 - - - +
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Residues in contact with LEU 154 (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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112C ILE* 3.3 24.6 - - + +
135C ILE* 5.1 4.3 - - + +
136C THR 3.2 28.0 - - - +
137C GLY* 3.4 19.5 - - - +
138C ARG 3.5 2.9 - - - +
139C ILE* 4.1 4.0 - - + -
152C PHE 4.2 1.0 - - - -
153C ASP* 1.3 71.8 - - - +
155C VAL* 1.3 61.3 + - - +
159C GLU 4.0 0.2 - - - +
160C LYS* 3.2 2.6 - - - -
161C ILE* 2.9 46.4 + - + +
163C VAL* 3.4 19.0 - - + +
190C VAL* 3.7 20.9 - - + -
192C ILE* 3.6 31.9 - - + -
206C ILE* 5.2 2.0 - - + -
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Residues in contact with VAL 155 (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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137C GLY* 3.6 2.9 - - - -
138C ARG* 2.9 35.5 + - + +
140C MET* 3.6 36.3 - - + -
153C ASP* 4.2 5.4 - - + +
154C LEU* 1.3 81.0 - - - +
156C GLY* 1.3 63.3 + - - +
158C GLY* 4.7 7.2 - - - +
159C GLU 3.4 20.2 - - - +
160C LYS* 4.0 13.0 - - + -
242C LEU* 5.8 7.4 - - + +
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Residues in contact with GLY 156 (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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112C ILE* 4.3 21.8 - - - +
113C PRO* 5.0 0.2 - - - +
137C GLY* 5.2 3.1 - - - -
155C VAL* 1.3 76.2 - - - +
157C ASP* 1.3 74.2 + - - +
158C GLY 3.1 3.1 - - - -
159C GLU* 2.9 22.6 + - - +
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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