Contacts of the strand formed by residues 153 - 164 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G SER* 3.7 9.6 - - - -
164G ARG* 2.9 24.1 + - - -
177G GLN* 3.1 25.9 + - - +
215G ILE* 4.5 2.0 - - + -
143I ALA 3.6 1.6 - - - +
144I VAL* 3.4 6.6 - - - +
145I GLY 2.9 28.5 + - - -
147I PRO* 3.7 31.9 - - + +
150I LEU* 4.7 1.9 - - - +
151I GLY 3.2 4.3 + - - -
152I GLN* 1.3 70.7 - - - +
154I ALA* 1.3 60.3 + - - +
155I THR* 4.0 22.0 - - + -
186I ASN* 5.2 0.9 - - - +
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Residues in contact with ALA 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G VAL* 3.9 25.8 - - + -
158G ILE* 3.4 15.9 - - + +
160G SER* 2.6 39.8 + - - -
19I LEU* 4.5 7.2 - - + -
23I LEU* 4.8 3.1 - - + -
142I VAL* 4.3 11.9 - - + -
143I ALA 3.2 7.0 - - - +
144I VAL* 4.3 8.7 - - + -
153I THR* 1.3 73.2 - - - +
155I THR* 1.3 58.2 + - - +
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Residues in contact with THR 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ILE* 3.9 3.8 - - - -
160G SER* 3.9 3.8 - - - +
179G ASP* 3.4 27.4 - - + -
214G GLY 4.4 4.5 - - - +
215G ILE* 5.4 2.7 - - + -
142I VAL* 3.3 5.4 - - - +
143I ALA* 2.8 47.1 + - - +
147I PRO* 6.1 0.4 - - + -
153I THR* 4.0 15.3 - - + -
154I ALA* 1.3 79.3 - - - +
156I SER* 1.3 59.5 + - - +
180I ALA* 4.3 0.7 - - - -
181I SER* 2.7 43.4 + - - +
186I ASN* 5.4 0.6 + - - +
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Residues in contact with SER 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 5.2 4.0 - - - -
157G GLY* 5.9 1.1 - - - -
158G ILE* 4.0 29.2 - - - +
179G ASP* 3.0 16.2 + - - +
15I LEU* 3.9 16.4 - - - +
140I PHE* 5.6 4.3 - - - +
141I ALA 3.6 8.9 + - - -
142I VAL* 4.5 1.2 - - - +
155I THR* 1.3 73.3 - - - +
157I GLY* 1.3 61.7 + - - +
179I ASP 4.6 1.2 - - - +
180I ALA* 3.7 12.7 - - - -
181I SER 4.8 0.2 + - - -
194I LEU* 6.1 0.2 - - - +
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Residues in contact with GLY 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H SER* 6.1 1.1 - - - -
140I PHE* 3.6 11.1 - - - +
141I ALA 2.9 29.1 + - - +
156I SER* 1.3 77.7 + - - +
158I ILE* 1.3 65.0 + - - +
178I THR* 4.6 0.9 - - - -
179I ASP* 3.3 13.2 - - - -
180I ALA* 3.8 9.5 - - - +
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Residues in contact with ILE 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.8 19.3 - - + -
19H LEU* 5.0 0.2 - - + -
142H VAL* 4.8 2.7 - - + -
154H ALA* 3.3 41.7 - - + +
155H THR* 3.9 5.8 - - - -
156H SER* 3.9 16.4 - - - +
138I GLY* 3.9 14.4 - - - +
139I ASP 3.3 7.0 - - - +
140I PHE* 3.7 31.6 - - + -
141I ALA* 4.5 2.9 - - - -
157I GLY* 1.3 73.4 - - - -
159I VAL* 1.3 72.7 + - - +
160I SER 3.3 3.1 + - - -
178I THR* 2.9 24.4 + - - -
179I ASP* 2.7 23.9 + - - +
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Residues in contact with VAL 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I LEU* 4.5 6.3 - - + -
136I ARG 3.7 20.2 - - - +
137I VAL* 3.6 5.8 - - - +
138I GLY 3.0 24.1 + - - -
139I ASP* 2.7 30.4 + - + +
140I PHE 5.0 0.2 - - - +
141I ALA* 4.4 6.3 - - + -
158I ILE* 1.3 75.8 - - - +
160I SER* 1.3 57.8 + - - +
161I ALA 3.9 6.7 - - - +
162I LEU* 3.8 34.1 - - + -
176I ILE* 4.1 11.2 - - + -
177I GLN 3.7 3.4 - - - -
178I THR* 4.8 1.3 - - - +
191I LEU* 5.5 0.2 - - + -
199I ILE* 4.2 24.9 - - + -
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Residues in contact with SER 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H GLN 4.0 1.9 - - - +
153H THR* 3.6 17.3 - - - -
154H ALA 2.8 42.3 + - - -
155H THR* 4.0 2.6 - - - +
137I VAL* 3.5 13.5 - - - +
158I ILE* 3.3 2.1 + - - +
159I VAL* 1.3 72.1 - - - +
161I ALA* 1.3 59.4 + - - +
177I GLN* 2.7 27.7 + - - -
178I THR 3.8 1.4 - - - -
179I ASP* 3.5 26.2 + - - +
214I GLY 4.8 0.6 + - - -
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Residues in contact with ALA 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H GLN 3.8 3.8 - - - +
153H THR* 4.7 0.2 - - - +
137I VAL* 3.8 9.6 - - - -
159I VAL* 3.7 2.2 - - - +
160I SER* 1.3 79.6 - - - +
162I LEU* 1.3 68.6 + - - +
164I ARG* 3.4 42.8 - - + +
175I PHE 4.8 0.4 - - - -
176I ILE* 3.7 1.7 - - - -
177I GLN* 2.9 37.8 + - + +
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Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I SER 5.0 3.4 - - - +
135I LEU* 3.5 42.2 - - + +
136I ARG* 3.8 11.2 - - - +
137I VAL* 4.0 13.8 - - + +
159I VAL* 3.8 18.8 - - + -
161I ALA* 1.3 78.5 - - - +
163I GLY* 1.3 65.3 + - - +
164I ARG* 3.3 10.2 + - - +
175I PHE 3.9 3.6 - - - -
176I ILE* 3.9 23.8 - - + -
293I LYS* 6.2 1.3 - - - +
296I ASN* 3.6 12.4 + - - +
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Residues in contact with GLY 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I LEU* 1.3 74.7 - - - +
164I ARG* 1.3 62.3 + - - +
165I SER* 3.5 8.0 + - - -
174I ASN* 3.2 31.5 + - - +
175I PHE 3.2 7.0 + - - -
176I ILE* 5.9 0.4 - - - +
296I ASN* 3.1 29.3 + - - +
300I GLU* 4.8 1.5 - - - +
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Residues in contact with ARG 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LEU* 3.4 33.9 + - - +
151H GLY* 3.0 20.4 + - - -
152H GLN 3.1 12.1 + - - +
153H THR* 2.8 28.9 + - - -
161I ALA* 3.4 23.9 - - + +
162I LEU 4.5 5.7 + - - +
163I GLY* 1.3 74.9 - - - +
165I SER* 1.3 62.7 + - - +
167I LEU* 4.4 13.5 - - + -
173I GLU* 3.8 0.2 - - - +
174I ASN 3.7 3.5 + - - -
175I PHE* 2.9 52.4 + - + +
177I GLN* 2.9 28.5 + - + +
217I PHE* 4.4 2.2 - - + -
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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