Contacts of the strand formed by residues 140 - 145 (chain C) in PDB entry 3STJ
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 PHE 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.2 30.7 + - + -
14B SER* 3.6 24.0 - - - -
15B LEU* 3.8 26.5 - - + -
156B SER* 5.1 3.8 - - - -
139C ASP* 1.3 77.6 - - - +
141C ALA* 1.3 59.4 + - - +
142C VAL* 6.3 0.2 - - + -
156C SER* 5.6 4.0 - - - +
157C GLY 3.6 7.2 - - - +
158C ILE* 3.7 24.0 - - + -
159C VAL* 5.2 0.4 - - - +
193C ASN* 3.9 19.3 - - - +
194C LEU* 3.8 34.1 + - + +
199C ILE* 4.8 2.6 - - - +
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Residues in contact with ALA 141 (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 ASP 3.8 0.4 + - - -
140C PHE* 1.3 75.0 - - - +
142C VAL* 1.3 65.5 + - - +
155C THR 4.2 0.2 - - - +
156C SER* 3.6 3.3 + - - -
157C GLY 2.9 35.0 + - - +
158C ILE 4.5 1.6 - - - -
159C VAL* 4.5 9.2 - - + -
178C THR* 4.2 13.0 - - - +
180C ALA* 4.5 1.5 - - - +
191C LEU* 3.9 22.4 - - + -
192C LEU 3.2 8.7 - - - +
199C ILE* 4.1 13.2 - - + -
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Residues in contact with VAL 142 (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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158A ILE* 4.8 2.9 - - + -
15C LEU* 3.8 27.1 - - + -
18C MET* 4.0 21.3 - - + -
19C LEU* 4.0 24.0 - - + -
140C PHE* 6.3 0.2 - - + -
141C ALA* 1.3 77.9 - - - +
143C ALA* 1.4 64.3 + - - +
144C VAL* 4.2 2.9 - - + -
154C ALA* 4.2 11.2 - - + -
155C THR 3.3 14.6 - - - +
156C SER* 4.4 3.6 - - - +
190C ALA 3.6 1.7 - - - +
191C LEU* 3.5 3.9 - - - -
192C LEU* 2.8 47.0 + - + +
193C ASN 4.9 0.2 - - - +
194C LEU* 4.9 6.7 - - + -
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Residues in contact with ALA 143 (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 ALA 4.2 0.6 - - - -
142C VAL* 1.4 71.8 - - - +
144C VAL* 1.3 60.4 + - - +
145C GLY 4.1 0.4 - - - -
153C THR 3.6 1.2 - - - +
154C ALA* 3.2 4.3 - - - -
155C THR* 2.8 53.5 + - - +
180C ALA* 4.1 8.9 - - + +
181C SER 4.4 0.4 - - - +
182C ILE* 4.0 19.1 - - + -
186C ASN* 4.5 4.6 - - - +
190C ALA 3.2 5.2 - - - -
191C LEU* 4.2 7.9 - - + +
202C ASN* 3.6 15.7 - - - +
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Residues in contact with VAL 144 (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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19C LEU* 4.3 1.1 - - + -
22C VAL* 5.7 0.2 - - + -
23C LEU* 3.6 33.0 - - + -
26C VAL* 3.5 25.5 - - + +
142C VAL* 4.2 10.8 - - + -
143C ALA* 1.3 76.0 - - - +
145C GLY* 1.3 60.4 + - - +
152C GLN* 3.7 25.8 - - + +
153C THR 3.4 4.5 - - - +
154C ALA* 4.3 3.4 - - + -
186C ASN* 4.5 1.8 - - - -
189C GLY* 3.7 2.1 - - - -
190C ALA* 2.7 36.5 + - + +
192C LEU* 3.8 27.6 - - + -
202C ASN* 4.3 0.9 - - - +
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Residues in contact with GLY 145 (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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26C VAL* 4.8 2.9 - - - -
66C SER* 3.4 16.6 - - - -
144C VAL* 1.3 75.5 - - - +
146C ASN* 1.3 58.4 + - - -
147C PRO* 3.4 8.0 - - - +
152C GLN* 3.5 6.2 - - - -
153C THR 2.8 33.5 + - - +
186C ASN* 3.8 15.9 + - - -
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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