Contacts of the strand formed by residues 149 - 159 (chain C) in PDB entry 4A12
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 THR 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.5 21.5 - - + -
95C LEU 3.4 20.4 - - - +
96C ASP* 3.1 22.5 + - + +
147C ASN 3.9 3.3 + - - -
148C ASP* 1.3 71.5 - - - +
150C VAL* 1.3 64.3 + - - +
151C ARG* 3.6 4.7 + - - +
171C TYR 3.7 6.1 - - - +
172C VAL* 3.9 13.2 - - - +
173C LYS 4.8 1.7 + - - -
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 3.3 3.5 - - - -
95C LEU* 2.8 38.6 + - + +
97C ILE* 3.8 17.9 - - + -
114C LEU* 3.7 16.2 - - + -
117C GLN* 3.1 31.1 + - - +
144C VAL* 3.7 30.1 - - + -
148C ASP 4.9 0.2 - - - +
149C THR* 1.3 71.7 - - - +
151C ARG* 1.3 59.4 + - - +
170C SER* 3.6 26.2 - - - -
171C TYR 3.5 7.0 - - - +
172C VAL* 3.9 7.4 - - + -
177C VAL* 4.5 3.8 - - + -
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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
----------------------------------------------------------
92C GLN* 3.3 43.2 - - + +
93C SER 3.7 2.5 - - - -
94C ILE* 4.4 11.2 - - + -
149C THR 3.6 2.4 + - - +
150C VAL* 1.3 70.2 - - - +
152C ALA* 1.3 59.5 + - - +
153C GLU* 3.6 17.6 + - - -
169C LYS 3.7 2.1 - - - +
170C SER* 3.4 1.8 - - - -
171C TYR* 2.8 86.8 + - - +
173C LYS 5.5 0.8 - - - +
174C HIS* 4.4 17.2 - - - +
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Residues in contact with ALA 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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92C GLN* 3.2 6.7 - - - +
93C SER* 2.9 34.8 + - - +
117C GLN* 3.5 27.6 - - + +
118C ALA* 5.3 1.6 - - - -
121C LEU* 3.4 16.6 - - + +
150C VAL 3.6 1.0 + - - -
151C ARG* 1.3 72.1 - - - +
153C GLU* 1.3 60.2 + - - +
168C VAL* 4.5 5.6 - - + -
169C LYS 3.7 0.2 - - - -
170C SER* 3.3 24.0 - - - +
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Residues in contact with GLU 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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90C LYS* 4.2 15.4 + - - -
91C ALA 3.4 7.2 - - - +
92C GLN* 3.7 21.3 + - + +
121C LEU* 4.1 1.1 - - - -
151C ARG* 3.6 21.8 + - - +
152C ALA* 1.3 74.3 - - - +
154C ALA* 1.3 59.9 + - - +
155C ARG* 2.8 39.5 + - - +
167C GLU 3.7 1.7 - - - +
168C VAL* 3.4 2.3 - - - -
169C LYS* 2.9 47.0 + - + +
171C TYR* 3.3 23.9 + - + -
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Residues in contact with ALA 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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90C LYS* 3.3 6.2 - - - +
91C ALA* 2.8 35.6 + - + +
121C LEU* 3.6 27.2 - - + +
122C CYS* 4.7 2.9 - - - -
125C LEU* 3.7 11.5 - - + +
153C GLU* 1.3 73.5 - - - +
155C ARG* 1.3 61.6 + - - +
166C VAL* 3.8 18.6 - - + -
167C GLU 3.4 4.7 - - - -
168C VAL* 3.8 10.5 - - + -
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Residues in contact with ARG 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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89C VAL 3.5 5.4 - - - +
90C LYS* 3.7 33.1 - - + +
125C LEU* 4.4 0.2 - - - -
153C GLU* 2.8 53.4 + - - +
154C ALA* 1.3 77.2 - - - +
156C VAL* 1.3 66.4 + - - +
157C VAL* 3.4 10.2 + - + +
166C VAL* 3.4 5.6 - - - +
167C GLU* 2.9 37.4 + - + +
169C LYS* 4.5 19.4 - - - +
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Residues in contact with VAL 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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88C ASN* 3.4 37.2 - - - +
89C VAL* 2.9 12.1 + - - +
125C LEU* 3.8 21.1 - - + -
126C ILE* 4.8 1.3 - - + -
155C ARG* 1.3 70.2 - - - +
157C VAL* 1.3 60.6 + - - +
158C ASN 3.5 24.9 - - - +
159C GLN* 4.8 2.9 - - + +
164C TYR* 3.7 25.4 - - + -
165C TYR 3.5 5.4 - - - +
166C VAL* 4.4 7.0 - - + +
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Residues in contact with VAL 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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155C ARG* 3.4 8.5 + - + +
156C VAL* 1.3 76.0 - - - +
158C ASN* 1.3 60.6 + - + +
165C TYR* 2.7 33.5 + - + +
166C VAL 4.4 0.9 - - - +
167C GLU* 3.7 50.5 - - + +
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Residues in contact with ASN 158 (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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156C VAL* 3.5 9.5 - - - +
157C VAL* 1.3 79.6 - - + +
159C GLN* 1.3 70.2 + - - +
160C THR* 4.0 12.1 - - - +
164C TYR 3.6 0.2 - - - -
165C TYR* 2.7 67.3 + - + +
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Residues in contact with GLN 159 (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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88C ASN* 5.3 1.2 - - - +
156C VAL* 4.8 2.9 - - + -
158C ASN* 1.3 86.0 + - - +
160C THR* 1.3 68.5 + - - +
163C HIS 3.4 10.1 - - - +
164C TYR* 3.0 44.8 + - + -
186C TYR* 3.2 24.4 + - - -
188C LYS* 5.7 1.4 - - - +
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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