Contacts of the strand formed by residues 150 - 157 (chain C) in PDB entry 3CMM
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 ARG 150 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 4.8 2.4 + - - -
124C GLN* 2.9 52.9 + - - +
125C VAL* 3.4 6.8 - - + +
126C VAL* 2.8 27.7 + - - +
148C GLY 4.1 15.6 + - - -
149C ILE* 1.3 73.7 - - - +
151C PHE* 1.3 58.7 + - - +
166C ASP 3.9 3.1 - - - -
167C LEU* 3.5 45.5 - - + +
171C PHE* 4.3 9.6 - - + -
377C ALA* 3.1 38.4 + - + +
378C CYS* 4.3 10.3 + - - +
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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
----------------------------------------------------------
126C VAL* 3.6 9.2 - - + -
128C ALA* 3.9 26.9 - - + -
137C LYS* 4.0 13.0 - - + -
140C ILE* 3.5 32.8 - - + -
141C ASN* 3.3 46.2 - - + +
144C CYS* 4.1 17.5 - - + -
145C HIS 5.6 0.2 - - - +
149C ILE 3.7 0.6 + - - +
150C ARG* 1.3 74.3 - - - +
152C ILE* 1.3 68.1 + - - +
153C SER* 3.8 22.0 - - - -
164C PHE* 4.1 15.0 - + - -
166C ASP* 2.8 44.0 + - - +
167C LEU* 4.3 0.2 - - - +
269C LEU* 4.5 4.5 - - + -
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Residues in contact with ILE 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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125C VAL* 4.2 12.1 - - + -
126C VAL 3.0 9.7 + - - +
127C VAL* 3.3 8.6 - - + +
128C ALA* 2.9 25.6 + - - +
151C PHE* 1.3 82.4 - - - +
153C SER* 1.3 69.0 + - - +
163C THR* 4.2 6.5 - - - +
164C PHE 3.3 10.5 - - - +
165C VAL* 4.2 20.0 - - + -
167C LEU* 4.5 4.3 - - + -
370C VAL* 3.7 27.4 - - + -
373C GLU* 3.8 13.7 - - + +
374C VAL* 3.7 40.6 - - + +
377C ALA* 4.5 6.3 - - + -
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Residues in contact with SER 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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127C VAL* 5.4 0.7 - - - -
128C ALA 3.3 4.9 - - - -
137C LYS* 3.1 36.5 + - - +
151C PHE* 3.8 19.7 - - - -
152C ILE* 1.3 77.9 - - - +
154C SER* 1.3 59.3 + - - +
162C ASN* 5.1 2.7 + - - -
163C THR* 3.0 8.3 + - - -
164C PHE* 2.7 52.1 + - - -
269C LEU* 5.4 2.6 - - - +
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Residues in contact with SER 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.6 19.0 - - - +
51C ILE* 4.8 3.6 - - - -
127C VAL* 5.4 1.1 - - - +
128C ALA 2.9 7.4 + - - +
129C THR* 3.3 17.4 - - - -
130C ASP 3.3 0.3 + - - -
137C LYS* 3.2 11.7 + - - -
153C SER* 1.3 77.5 + - - +
155C GLU* 1.3 67.1 + - - +
162C ASN* 3.0 20.1 + - - -
163C THR* 4.2 0.4 - - - +
366C PHE* 3.8 10.4 - - - +
370C VAL* 3.7 31.5 - - - +
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Residues in contact with GLU 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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47C LEU* 3.8 8.5 - - - -
130C ASP* 4.0 13.0 - - + -
134C LEU* 5.8 1.9 - - - +
137C LYS* 4.0 15.3 + - - +
154C SER* 1.3 80.4 + - - +
156C THR* 1.3 63.5 + - - +
157C ARG* 3.2 29.4 + - - +
161C GLY* 3.3 2.8 - - - -
162C ASN* 3.0 56.9 + - - +
296C PHE* 3.4 18.5 - - + +
300C HIS* 3.1 31.5 + - - -
366C PHE* 5.0 0.7 - - - -
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Residues in contact with THR 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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47C LEU* 4.3 12.4 - - - +
130C ASP* 4.1 8.9 - - - +
155C GLU* 1.3 76.3 + - - +
157C ARG* 1.3 85.4 + - - +
158C GLY 4.1 15.0 - - - +
160C PHE 3.5 4.3 - - - -
161C GLY* 4.2 0.2 - - - -
357C GLY 4.5 4.4 - - - +
358C ASP* 4.8 4.0 - - - +
359C ILE 4.7 6.7 - - - +
362C VAL* 3.7 23.3 + - + +
363C VAL* 3.8 30.2 - - + +
366C PHE* 4.2 10.7 - - - +
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Residues in contact with ARG 157 (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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130C ASP* 3.6 38.0 + - - +
155C GLU* 3.2 26.2 + - - +
156C THR* 1.3 89.5 + - - +
158C GLY* 1.3 64.3 + - - +
159C LEU 3.4 0.7 + - - -
160C PHE* 2.9 31.5 + - - +
296C PHE* 3.5 24.2 - - + -
299C LEU* 3.8 23.6 - - + -
300C HIS* 4.7 7.0 + - - -
310C LEU* 3.9 30.2 - - - +
351C LEU* 4.7 5.4 - - + -
354C GLN 3.4 6.0 - - - +
355C ALA* 3.8 24.4 + - - +
357C GLY 3.9 4.6 + - - -
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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