Contacts of the strand formed by residues 145 - 152 (chain C) in PDB entry 3H0Z
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 GLY 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C GLY 4.5 0.9 - - - +
141C LYS 4.2 1.9 - - - -
142C GLY* 3.9 11.0 + - - -
144C PHE* 1.3 83.3 - - - +
146C ASN* 1.3 69.3 + - - -
147C VAL 4.3 0.2 + - - -
162C LYS* 5.2 9.5 - - - -
163C VAL 3.1 20.4 - - - -
164C LEU* 4.0 7.7 - - - +
165C PHE* 5.2 1.8 - - - -
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Residues in contact with ASN 146 (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 PRO* 5.0 2.7 - - + -
140C GLY 3.5 7.6 - - - +
141C LYS* 3.2 35.9 - - + +
142C GLY 3.3 14.5 + - - +
145C GLY* 1.3 77.1 - - - -
147C VAL* 1.3 61.5 + - - +
148C TYR* 3.3 39.2 + - + +
162C LYS* 3.8 2.6 - - - -
163C VAL* 3.1 27.6 + - - +
165C PHE* 5.3 8.4 - - - -
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Residues in contact with VAL 147 (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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1C 45B 3.2 64.8 - - + +
138C PRO* 3.6 1.4 - - - +
139C LEU* 2.7 37.8 + - + +
140C GLY 3.0 18.7 + - - +
145C GLY 4.3 0.2 + - - -
146C ASN* 1.3 72.9 - - - +
148C TYR* 1.3 56.8 + - - +
160C ALA* 4.0 15.9 - - + -
161C LEU 3.5 11.0 - - - +
162C LYS* 4.2 14.4 - - + +
210C LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 148 (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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135C ILE* 4.0 26.5 - - + -
136C GLY 3.7 14.8 - - - +
137C ARG 3.7 1.6 - - - -
138C PRO* 3.8 31.2 - - + -
139C LEU* 4.1 2.9 - - - -
146C ASN* 3.3 40.3 + - + -
147C VAL* 1.3 72.9 - - - +
149C LEU* 1.3 62.5 + - - +
160C ALA* 3.4 3.8 - - - -
161C LEU* 2.8 55.0 + - + +
163C VAL* 3.9 21.3 - - + -
205C ARG* 5.9 2.3 + - - -
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Residues in contact with LEU 149 (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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135C ILE* 3.6 1.7 - - - -
136C GLY* 2.6 39.2 + - - +
137C ARG* 3.0 34.7 + - + +
139C LEU* 3.8 27.7 - - + +
148C TYR* 1.3 73.2 - - - +
150C ALA* 1.3 71.3 + - - +
151C ARG* 5.6 0.9 - - + +
158C ILE* 3.7 25.4 - - + -
159C LEU 4.1 2.7 - - - +
212C TYR* 4.3 25.1 - - + +
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Residues in contact with ALA 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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133C PHE* 4.7 15.0 - - + -
134C GLU 3.3 11.7 - - - +
135C ILE* 5.1 2.7 - - + -
136C GLY 4.7 0.2 - - - +
148C TYR* 3.4 0.4 + - + -
149C LEU* 1.3 81.8 - - - +
151C ARG* 1.3 64.7 + - - +
158C ILE* 3.6 4.2 - - - -
159C LEU* 2.9 39.5 + - + +
160C ALA 4.4 0.4 - - - -
161C LEU* 3.9 29.2 - - + +
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Residues in contact with ARG 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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133C PHE* 3.7 4.4 - - - -
134C GLU* 2.7 70.3 + - + +
149C LEU* 5.6 1.0 - - + +
150C ALA* 1.3 78.0 - - - +
152C GLU* 1.3 63.2 + - - +
153C LYS 3.4 0.2 + - - -
156C LYS* 3.2 45.9 - - - +
157C PHE 3.2 11.2 - - - +
158C ILE* 3.6 24.9 - - + +
159C LEU* 4.5 0.9 - - - +
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Residues in contact with GLU 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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128C TRP* 3.4 34.0 - - + -
132C ASP* 3.5 18.5 - - - +
133C PHE* 4.1 18.1 - - + -
134C GLU* 5.4 0.2 - - - -
151C ARG* 1.3 70.6 - - - +
153C LYS* 1.3 70.3 + - - +
154C GLN* 2.8 40.9 + - - +
155C SER* 3.1 21.4 + - - +
156C LYS* 2.8 26.3 + - - -
157C PHE 3.4 7.9 + - - -
159C LEU* 4.3 12.7 - - + +
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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