Contacts of the strand formed by residues 153 - 164 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU* 5.8 0.2 - - - -
143B ALA 3.6 1.2 - - - +
144B VAL* 3.4 6.5 - - - +
145B GLY 2.9 29.3 + - - -
147B PRO* 3.6 29.5 - - + +
150B LEU* 4.6 1.7 - - - +
151B GLY 3.2 3.5 + - - -
152B GLN* 1.3 71.7 - - - +
154B ALA* 1.3 61.6 + - - +
155B THR* 4.0 17.2 + - + +
186B ASN* 5.2 0.5 - - - +
160C SER* 3.7 14.4 - - - -
164C ARG* 2.8 24.8 + - - -
177C GLN* 3.1 25.9 + - - +
215C ILE* 4.5 2.7 - - + -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.0 18.8 - - + -
23B LEU* 4.5 4.7 - - + +
142B VAL* 4.2 4.5 - - + -
143B ALA 3.2 7.9 - - - +
144B VAL* 4.3 8.3 - - + -
153B THR* 1.3 72.6 - - - +
155B THR* 1.3 57.7 + - - +
137C VAL* 3.8 25.4 - - + -
158C ILE* 3.4 9.7 - - + +
160C SER* 2.7 39.4 + - - -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 3.3 4.7 - - - +
143B ALA* 2.7 47.1 + - - +
147B PRO* 6.0 0.9 - - + -
153B THR* 4.0 15.5 - - + +
154B ALA* 1.3 78.6 - - - +
156B SER* 1.3 59.9 + - - +
180B ALA* 4.1 1.5 - - - +
181B SER* 2.6 42.9 + - - +
186B ASN* 5.3 1.1 + - - +
158C ILE* 4.0 3.8 - - - -
160C SER* 3.9 3.6 - - - +
179C ASP* 3.5 27.1 - - + -
214C GLY 4.3 4.5 - - - +
215C ILE* 5.4 2.5 - - + -
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Residues in contact with SER 156 (chain B).
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 - - - +
140B PHE* 5.7 4.0 - - - +
141B ALA 3.6 8.6 + - - -
142B VAL* 4.4 2.2 - - - +
155B THR* 1.3 73.9 - - - +
157B GLY* 1.3 62.5 + - - +
179B ASP 4.6 1.6 - - - +
180B ALA* 3.7 12.1 - - - -
181B SER 4.7 0.2 + - - -
140C PHE* 5.1 3.7 - - - -
157C GLY* 5.8 1.3 - - - -
158C ILE* 3.9 31.3 - - - +
179C ASP* 2.9 16.9 + - - +
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Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER* 5.8 1.8 - - - -
140B PHE* 3.6 11.2 - - - +
141B ALA 2.9 29.0 + - - +
156B SER* 1.3 77.8 + - - +
158B ILE* 1.3 64.5 + - - +
178B THR* 4.6 0.9 - - - -
179B ASP* 3.3 13.5 - - - -
180B ALA* 3.8 9.3 - - - +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 10.5 - - + -
19A LEU* 5.0 0.4 - - + -
142A VAL* 4.9 2.5 - - + -
154A ALA* 3.4 40.2 - - + +
155A THR* 4.0 9.6 - - - -
156A SER* 4.0 17.0 - - - +
138B GLY* 3.8 18.8 - - - +
139B ASP 3.3 7.6 - - - +
140B PHE* 3.7 28.9 - - + -
141B ALA* 4.3 2.7 - - - +
157B GLY* 1.3 75.3 - - - -
159B VAL* 1.4 70.1 + - - +
160B SER* 3.4 1.1 + - - +
178B THR* 2.9 28.6 + - - -
179B ASP* 2.7 24.9 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.5 6.1 - - + -
136B ARG 3.6 20.0 - - - +
137B VAL* 3.4 6.8 - - - +
138B GLY* 2.9 24.4 + - - -
139B ASP* 2.7 29.2 + - + +
140B PHE 5.2 0.2 - - - +
141B ALA* 4.5 5.4 - - + -
158B ILE* 1.4 71.5 - - - +
160B SER* 1.4 58.0 + - - +
161B ALA 3.7 21.5 - - - +
162B LEU* 3.7 23.6 - - + -
176B ILE* 4.0 11.9 - - + -
177B GLN 3.7 2.7 - - - -
178B THR* 4.8 0.7 - - - +
191B LEU* 5.4 0.4 - - + -
199B ILE* 4.2 24.7 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLN 3.9 1.9 - - - +
153A THR* 3.6 18.0 - - - -
154A ALA 2.7 44.6 + - - -
155A THR* 4.0 2.0 - - - +
137B VAL* 3.6 12.0 - - - +
158B ILE* 3.4 1.9 + - - +
159B VAL* 1.4 71.9 - - - +
161B ALA* 1.4 59.5 + - - +
177B GLN* 2.7 26.5 + - - -
178B THR 3.8 1.5 - - - -
179B ASP* 3.5 26.3 + - - +
214B GLY 5.0 0.3 + - - -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLN 3.7 4.3 - - - +
137B VAL* 3.8 10.1 - - - +
159B VAL* 3.6 4.8 - - - +
160B SER* 1.4 79.5 - - - +
162B LEU* 1.3 69.6 + - - +
164B ARG* 3.4 42.2 - - + +
175B PHE 4.8 0.2 - - - -
176B ILE* 3.8 0.5 - - - -
177B GLN* 2.9 37.0 + - + +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER 5.0 2.5 - - - +
135B LEU* 3.4 39.0 - - + +
136B ARG* 3.8 16.2 - - - -
137B VAL* 3.9 14.3 - - + +
159B VAL* 3.7 19.3 - - + -
161B ALA* 1.3 79.6 - - - +
163B GLY* 1.3 65.3 + - - +
164B ARG* 3.3 10.4 + - - +
175B PHE 3.9 3.6 - - - -
176B ILE* 3.9 23.3 - - + -
293B LYS* 6.2 1.3 - - - +
296B ASN* 3.6 13.2 + - - +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU* 1.3 75.8 - - - +
164B ARG* 1.3 61.8 + - - +
165B SER* 3.6 8.0 + - - -
174B ASN* 3.1 31.0 + - - -
175B PHE 3.2 7.7 + - - -
176B ILE* 5.9 0.2 - - - +
296B ASN* 3.1 29.0 - - - +
297B SER* 4.8 0.9 + - - -
300B GLU* 4.8 2.1 - - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.5 32.4 + - - +
151A GLY* 3.1 20.2 + - - -
152A GLN 3.2 12.1 + - - +
153A THR* 2.8 28.9 + - - -
161B ALA* 3.4 25.0 - - + +
162B LEU 4.4 5.5 + - - +
163B GLY* 1.3 75.3 - - - +
165B SER* 1.3 65.0 + - - +
167B LEU* 4.4 18.2 - - + -
174B ASN 3.7 2.9 + - - -
175B PHE* 2.9 52.0 + - + +
177B GLN* 2.9 26.9 + - + +
217B PHE* 4.4 3.1 - - + -
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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