Contacts of the strand formed by residues 153 - 164 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143K ALA 3.6 1.2 - - - +
144K VAL* 3.3 7.3 - - - +
145K GLY 2.8 28.5 + - - -
147K PRO* 3.6 29.3 - - + +
150K LEU* 4.5 1.4 - - - +
151K GLY 3.0 5.5 + - - -
152K GLN* 1.3 71.9 - - - +
154K ALA* 1.3 61.3 + - - +
155K THR* 4.1 15.7 - - + +
186K ASN* 5.2 1.2 - - - +
160L SER* 3.7 15.9 - - - -
164L ARG* 2.8 25.6 + - - -
177L GLN* 3.2 25.7 + - - +
215L ILE* 4.5 2.0 - - + -
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Residues in contact with ALA 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 4.5 5.8 - - + -
23K LEU* 4.7 4.7 - - + -
142K VAL* 4.3 11.2 - - + -
143K ALA 3.2 6.1 - - - +
144K VAL* 4.4 9.4 - - + +
153K THR* 1.3 71.9 - - - +
155K THR* 1.3 56.5 + - - +
137L VAL* 3.8 26.7 - - + +
158L ILE* 3.4 14.5 - - + +
160L SER* 2.7 39.0 + - - -
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Residues in contact with THR 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K VAL* 3.3 4.2 - - - +
143K ALA* 2.7 47.8 + - - +
153K THR* 4.1 15.0 - - + -
154K ALA* 1.3 79.2 - - - +
156K SER* 1.3 59.1 + - - +
180K ALA* 4.1 1.2 - - - +
181K SER* 2.7 42.4 + - - +
186K ASN* 5.2 0.9 + - - -
158L ILE* 4.0 4.0 - - - -
160L SER* 4.0 3.6 - - - +
179L ASP* 3.6 27.1 - - + -
214L GLY 4.4 5.2 - - - +
215L ILE* 5.3 2.7 - - + -
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Residues in contact with SER 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 3.9 16.5 - - - +
140K PHE* 5.7 4.2 - - - +
141K ALA 3.6 8.5 + - - -
142K VAL* 4.4 2.7 - - - +
155K THR* 1.3 73.6 - - - +
157K GLY* 1.3 61.7 + - - +
179K ASP 4.6 1.6 - - - +
180K ALA* 3.7 12.6 - - - -
181K SER 4.7 0.2 + - - -
140L PHE* 5.3 3.3 - - - -
157L GLY* 5.9 1.1 - - - -
158L ILE* 4.0 29.9 - - - +
179L ASP* 3.0 16.8 + - - +
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Residues in contact with GLY 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J SER* 5.9 1.1 - - - -
140K PHE* 3.6 11.0 - - - +
141K ALA* 2.9 28.4 + - - +
156K SER* 1.3 78.6 + - - +
158K ILE* 1.3 65.3 + - - +
178K THR* 4.6 0.9 - - - -
179K ASP* 3.3 13.2 - - - -
180K ALA* 3.9 9.3 - - - +
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Residues in contact with ILE 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 4.0 8.5 - - + -
19J LEU* 5.1 0.2 - - + -
142J VAL* 4.8 2.7 - - + -
154J ALA* 3.4 40.4 - - + +
155J THR* 3.9 6.5 - - - -
156J SER* 3.9 22.7 - - - +
138K GLY* 3.9 18.6 - - - +
139K ASP 3.3 6.7 - - - +
140K PHE* 3.7 33.0 - - + -
141K ALA* 4.3 2.9 - - - +
157K GLY* 1.3 72.8 - - - -
159K VAL* 1.4 71.6 + - - +
160K SER 3.4 0.9 + - - -
178K THR* 2.8 28.8 + - - -
179K ASP* 2.7 23.3 + - - +
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Residues in contact with VAL 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K LEU* 4.5 6.1 - - + -
136K ARG 3.7 18.4 - - - +
137K VAL* 3.5 9.1 - - - +
138K GLY* 2.9 24.8 + - - -
139K ASP* 2.7 28.1 + - + +
141K ALA* 4.5 5.2 - - + -
158K ILE* 1.4 73.4 - - - +
160K SER* 1.3 59.3 + - - +
161K ALA 3.7 18.4 - - - +
162K LEU* 3.8 24.9 - - + -
176K ILE* 4.0 11.9 - - + -
177K GLN 3.7 3.4 - - - -
178K THR* 4.8 1.1 - - - +
199K ILE* 4.2 25.4 - - + -
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Residues in contact with SER 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J GLN 4.1 1.6 - - - +
153J THR* 3.6 7.6 - - - -
154J ALA 2.7 45.4 + - - -
155J THR* 3.9 2.1 - - - +
137K VAL* 3.5 11.7 - - - +
158K ILE* 3.4 2.7 + - - +
159K VAL* 1.3 72.6 - - - +
161K ALA* 1.3 59.3 + - - +
177K GLN* 2.7 36.9 + - - -
178K THR* 3.8 1.2 - - - -
179K ASP* 3.5 26.9 + - - +
214K GLY 4.9 0.4 + - - -
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Residues in contact with ALA 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J GLN 3.8 4.0 - - - +
137K VAL* 3.8 9.6 - - - +
159K VAL* 3.6 4.7 - - - +
160K SER* 1.3 77.7 - - - +
162K LEU* 1.3 68.2 + - - +
164K ARG* 3.4 42.6 - - + +
175K PHE 4.9 0.4 - - - -
176K ILE 3.8 0.7 - - - -
177K GLN* 2.8 38.5 + - + +
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Residues in contact with LEU 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K SER 5.0 3.1 - - - +
135K LEU* 3.4 44.2 - - + +
136K ARG* 3.8 11.7 - - - -
137K VAL* 4.0 14.3 - - + +
159K VAL* 3.8 18.4 - - + -
161K ALA* 1.3 78.3 - - - +
163K GLY* 1.3 64.0 + - - +
164K ARG* 3.3 11.3 + - - +
175K PHE 3.9 3.8 - - - -
176K ILE* 4.0 21.5 - - + -
293K LYS* 6.2 1.1 - - - +
296K ASN* 3.5 12.7 + - - +
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Residues in contact with GLY 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162K LEU* 1.3 75.7 - - - +
164K ARG* 1.3 59.3 + - - +
165K SER* 3.2 17.2 + - - -
174K ASN* 3.2 27.1 + - - +
175K PHE 3.2 6.6 + - - -
296K ASN* 3.2 26.8 - - - +
297K SER* 4.7 0.5 + - - -
300K GLU* 4.8 2.1 - - - +
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Residues in contact with ARG 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J LEU* 3.5 33.4 + - - +
151J GLY* 3.0 18.8 + - - -
152J GLN 3.1 11.9 + - - +
153J THR* 2.7 29.7 + - - -
161K ALA* 3.4 24.9 - - + +
162K LEU 4.5 6.1 + - - +
163K GLY* 1.3 75.0 - - - +
165K SER* 1.3 61.2 + - - +
167K LEU* 4.4 11.2 - - + -
174K ASN 3.7 1.9 + - - -
175K PHE* 2.9 59.3 + - + +
177K GLN* 2.9 26.8 + - + +
217K PHE* 4.2 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