Contacts of the strand formed by residues 153 - 164 (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 THR 153 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER* 3.6 15.9 - - - -
164A ARG* 2.7 27.0 + - - -
177A GLN* 3.3 25.0 + - - +
215A ILE* 4.7 1.8 - - + -
143C ALA 3.6 1.0 - - - +
144C VAL* 3.4 4.4 - - - -
145C GLY 2.8 28.4 + - - -
147C PRO* 3.7 29.7 - - + +
150C LEU* 4.7 0.7 - - - +
151C GLY 3.2 3.6 + - - -
152C GLN* 1.3 73.0 - - - +
154C ALA* 1.3 60.9 + - - +
155C THR* 4.0 17.0 - - + -
186C ASN* 5.2 1.1 - - - +
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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
----------------------------------------------------------
137A VAL* 3.8 25.4 - - + -
158A ILE* 3.4 14.9 - - + +
160A SER* 2.7 39.0 + - - -
19C LEU* 4.3 5.8 - - + -
23C LEU* 4.6 4.5 - - + -
142C VAL* 4.2 11.9 - - + -
143C ALA 3.2 7.6 - - - +
144C VAL* 4.3 9.6 - - + +
153C THR* 1.3 72.8 - - - +
155C THR* 1.3 57.4 + - - +
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Residues in contact with THR 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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158A ILE* 4.0 3.6 - - - -
160A SER* 4.0 4.0 - - - +
179A ASP* 3.5 26.7 - - + -
214A GLY 4.3 5.4 - - - +
215A ILE* 5.4 2.7 - - + -
142C VAL* 3.3 5.4 - - - +
143C ALA* 2.8 46.6 + - - +
147C PRO* 6.1 0.4 - - + -
153C THR* 4.0 15.0 - - + +
154C ALA* 1.3 78.8 - - - +
156C SER* 1.3 59.7 + - - +
180C ALA* 4.1 1.3 - - - +
181C SER* 2.7 43.6 + - - +
186C ASN* 5.0 2.6 + - - +
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Residues in contact with SER 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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140A PHE* 5.2 3.2 - - - -
157A GLY* 6.0 0.9 - - - -
158A ILE* 4.0 29.7 - - - +
179A ASP* 2.9 15.9 + - - +
15C LEU* 3.8 16.1 - - - +
140C PHE* 5.6 4.5 - - - +
141C ALA 3.6 8.2 + - - -
142C VAL* 4.4 1.6 - - - +
155C THR* 1.3 74.8 - - - +
157C GLY* 1.3 62.3 + - - +
179C ASP 4.6 1.9 - - - +
180C ALA* 3.7 13.5 - - - -
181C SER 4.7 0.3 + - - -
194C LEU* 6.2 0.2 - - - +
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Residues in contact with GLY 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B SER* 6.1 1.6 - - - -
140C PHE* 3.6 10.9 - - - +
141C ALA 2.9 29.9 + - - +
156C SER* 1.3 77.8 + - - +
158C ILE* 1.3 65.1 + - - +
178C THR* 4.6 1.1 - - - -
179C ASP* 3.3 13.0 - - - -
180C ALA* 3.9 8.9 - - - +
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Residues in contact with ILE 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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15B LEU* 3.9 15.7 - - + -
19B LEU* 4.9 0.2 - - + -
142B VAL* 4.7 3.1 - - + -
154B ALA* 3.4 41.3 - - + +
155B THR* 4.0 1.3 - - - -
156B SER* 3.9 25.8 - - - +
138C GLY* 3.9 12.8 - - - +
139C ASP 3.3 7.6 - - - +
140C PHE* 3.7 30.1 - - + -
141C ALA* 4.2 2.9 - - - +
157C GLY* 1.3 75.5 - - - -
159C VAL* 1.4 72.0 + - - +
160C SER 3.4 0.7 + - - -
178C THR* 2.8 28.6 + - - -
179C ASP* 2.7 23.3 + - - +
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Residues in contact with VAL 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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135C LEU* 4.6 7.2 - - + -
136C ARG 3.7 17.5 - - - +
137C VAL* 3.4 8.1 - - - +
138C GLY* 2.9 24.6 + - - -
139C ASP* 2.7 29.1 + - + +
140C PHE 5.2 0.2 - - - +
141C ALA* 4.5 5.6 - - + -
158C ILE* 1.4 73.6 - - - +
160C SER* 1.3 59.3 + - - +
161C ALA 3.7 10.5 - - - +
162C LEU* 3.7 33.4 - - + -
176C ILE* 4.0 13.0 - - + -
177C GLN 3.7 3.4 - - - -
178C THR* 4.8 0.7 - - - +
199C ILE* 4.3 24.2 - - + -
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Residues in contact with SER 160 (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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152B GLN 4.1 1.2 - - - +
153B THR* 3.7 18.2 - - - -
154B ALA 2.7 44.7 + - - -
155B THR* 3.9 2.6 - - - +
137C VAL* 3.5 12.3 - - - +
158C ILE* 3.4 2.0 + - - +
159C VAL* 1.3 71.7 - - - +
161C ALA* 1.3 59.5 + - - +
177C GLN* 2.7 26.9 + - - -
178C THR 3.8 1.6 - - - -
179C ASP* 3.5 26.9 + - - +
214C GLY 5.0 0.6 + - - -
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Residues in contact with ALA 161 (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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152B GLN 3.8 3.4 - - - +
153B THR* 4.7 0.2 - - - +
137C VAL* 3.8 9.6 - - - -
159C VAL* 3.6 3.6 - - - +
160C SER* 1.3 78.9 - - - +
162C LEU* 1.3 68.1 + - - +
164C ARG* 3.4 42.4 - - + +
176C ILE* 3.7 1.7 - - - -
177C GLN* 2.8 38.8 + - + +
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Residues in contact with LEU 162 (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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132C SER 5.0 2.9 - - - +
135C LEU* 3.4 43.1 - - + +
136C ARG* 3.8 11.2 - - - -
137C VAL* 4.0 14.1 - - + +
159C VAL* 3.7 19.1 - - + -
161C ALA* 1.3 78.0 - - - +
163C GLY* 1.3 65.2 + - - +
164C ARG* 3.3 11.7 + - - +
175C PHE 3.9 3.6 - - - -
176C ILE* 3.9 23.6 - - + -
296C ASN* 3.5 13.5 + - - +
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Residues in contact with GLY 163 (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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162C LEU* 1.3 75.2 - - - +
164C ARG* 1.3 61.5 + - - +
165C SER* 3.5 8.1 + - - -
174C ASN* 3.1 31.4 + - - -
175C PHE 3.2 7.0 + - - -
176C ILE* 5.9 0.2 - - - +
296C ASN* 3.1 28.2 - - - +
297C SER* 4.8 0.7 + - - -
300C GLU* 4.8 2.4 - - - +
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Residues in contact with ARG 164 (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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150B LEU* 3.4 30.5 + - - +
151B GLY* 3.0 14.6 + - - -
152B GLN 3.0 18.0 + - - +
153B THR* 2.8 28.5 + - - -
161C ALA* 3.4 25.5 - - + +
162C LEU 4.5 6.7 + - - +
163C GLY* 1.3 73.2 - - - +
165C SER* 1.3 63.9 + - - +
167C LEU* 4.4 11.7 - - + -
173C GLU* 3.8 0.2 - - - +
174C ASN 3.7 3.8 + - - -
175C PHE* 2.9 51.5 + - + +
177C GLN* 2.9 23.0 + - + +
217C PHE* 4.4 12.3 - - + -
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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