Contacts of the strand formed by residues 193 - 203 (chain B) in PDB entry 4KMH
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 GLY 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLY 3.4 6.2 + - - -
110B THR* 3.5 17.4 - - - +
112B GLY 3.6 6.5 - - - -
113B PRO 4.2 0.4 - - - -
114B SER* 3.5 8.7 - - - -
189B GLN* 3.3 6.5 + - - -
190B THR* 2.8 36.0 + - - +
191B PRO 3.5 0.4 - - - -
192B PHE* 1.3 80.4 - - - +
194B VAL* 1.3 58.0 + - - -
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Residues in contact with VAL 194 (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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110B THR 4.3 2.9 - - - +
112B GLY 2.9 25.4 + - - +
113B PRO* 3.8 2.1 - - + +
114B SER* 3.0 17.8 + - - +
117B GLY* 3.6 13.0 - - - +
187B PRO* 5.0 6.7 - - + -
188B VAL 3.5 11.0 - - - +
189B GLN* 3.4 25.6 - - + +
193B GLY* 1.3 72.1 - - - -
195B VAL* 1.3 71.5 + - - +
196B THR* 4.2 11.2 - - + -
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Residues in contact with VAL 195 (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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37B ILE* 4.6 5.8 - - + -
96B SER* 3.8 14.4 - - - +
114B SER* 3.7 19.7 - - - +
117B GLY 3.8 1.8 - - - -
118B PHE* 4.0 7.2 - - - -
119B GLU* 3.9 25.4 - - + -
187B PRO* 3.2 3.5 - - - +
188B VAL* 2.8 48.7 + - + +
190B THR* 3.8 21.8 - - + -
194B VAL* 1.3 76.2 - - - +
196B THR* 1.3 75.0 + - - +
197B PHE* 3.9 12.3 - - + -
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Residues in contact with THR 196 (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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117B GLY 3.0 19.3 + - - +
118B PHE* 3.2 10.2 - - - +
119B GLU 3.2 22.0 + - - -
187B PRO* 4.2 23.1 - - + -
194B VAL* 4.7 9.4 - - + -
195B VAL* 1.3 81.4 - - - +
197B PHE* 1.3 67.6 + - - +
198B LEU* 5.1 4.7 - - - +
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Residues in contact with PHE 197 (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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37B ILE* 3.8 27.1 - - + -
40B GLU* 4.7 3.1 - - + -
91B ILE* 4.9 1.8 - - + -
119B GLU* 3.6 21.3 - - + -
121B THR* 4.2 10.3 - - + -
181B GLU* 3.6 5.7 - - - +
182B ASP* 3.0 31.2 + - + -
185B MET* 3.5 56.3 - - + +
186B GLN 3.3 29.6 - - - -
187B PRO* 4.4 1.6 - - - +
188B VAL* 4.1 18.4 - - + -
195B VAL* 3.9 16.2 - - + -
196B THR* 1.3 81.9 - - - +
198B LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 198 (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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118B PHE* 3.8 32.1 - - + +
119B GLU 3.2 6.5 + - - -
120B LEU* 3.3 12.4 - - + +
121B THR* 2.7 32.0 + - - +
155B PHE* 3.3 42.6 - - + +
156B CYS* 3.8 6.1 - - - +
157B SER* 3.6 30.5 - - - +
179B LEU* 4.5 11.2 - - + -
180B THR 3.3 13.7 - - - +
181B GLU* 4.8 1.8 - - + +
196B THR* 4.1 5.5 - - - +
197B PHE* 1.3 73.0 - - - +
199B GLN* 1.3 55.7 + - - +
200B ILE 3.9 0.3 + - - -
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Residues in contact with GLN 199 (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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121B THR* 3.2 20.6 - - - +
122B PHE* 4.5 1.8 - - - -
123B ARG* 3.1 25.6 + - - +
178B LEU 3.5 0.5 - - - +
179B LEU* 3.4 7.4 - - - -
180B THR* 2.6 47.7 + - + +
182B ASP* 3.7 8.4 - - - +
183B PRO* 3.1 26.8 - - - +
197B PHE 3.7 1.2 + - - -
198B LEU* 1.3 72.1 - - - +
200B ILE* 1.3 73.2 + - - +
201B VAL* 4.2 0.6 - - - +
233B TRP 3.0 12.7 + - - -
234B LEU* 2.7 36.8 + - - +
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Residues in contact with ILE 200 (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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120B LEU* 3.9 24.9 - - + -
121B THR 2.8 21.2 + - - +
122B PHE* 3.2 37.3 - - + -
123B ARG 4.5 0.2 + - - -
140B LEU* 4.8 8.3 - - + -
141B MET* 3.9 26.2 - - + -
144B LEU* 3.8 20.6 - - + -
167B LEU* 5.4 0.2 - - + -
177B MET* 3.6 35.2 - - + -
178B LEU 3.5 4.5 - - - -
179B LEU* 3.9 8.1 - - + -
199B GLN* 1.3 82.2 + - - +
201B VAL* 1.3 65.1 + - - +
202B GLY* 4.7 0.4 - - - +
234B LEU 4.8 0.5 - - - +
236B THR* 4.3 1.0 + - - -
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Residues in contact with VAL 201 (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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177B MET* 3.2 4.3 - - - -
178B LEU* 2.7 49.4 + - + +
180B THR* 3.7 28.9 - - + -
199B GLN* 3.9 3.8 - - - +
200B ILE* 1.3 80.1 - - - +
202B GLY* 1.3 71.7 + - - +
203B VAL* 4.3 1.2 - - + +
220B LEU* 4.4 6.1 - - + -
223B LEU* 4.6 14.6 - - + -
230B GLY 5.7 4.3 - - - +
234B LEU* 3.8 42.8 - - + +
235B ILE 5.7 0.4 - - - -
236B THR* 3.8 5.6 - - - +
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Residues in contact with GLY 202 (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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122B PHE* 4.6 2.0 - - - -
167B LEU* 4.0 10.3 - - - -
174B ILE* 3.4 22.8 - - - +
176B HIS 3.2 9.6 - - - -
200B ILE* 4.2 1.0 - - - +
201B VAL* 1.3 76.4 - - - +
203B VAL* 1.3 66.0 + - - +
223B LEU* 5.6 0.7 - - - +
229B ALA 5.3 3.1 - - - +
236B THR* 2.9 20.9 + - - +
240B ARG* 4.0 10.0 + - - -
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Residues in contact with VAL 203 (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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174B ILE* 3.5 6.6 - - - +
175B GLN 3.3 3.5 + - - -
176B HIS* 2.7 58.1 + - + -
177B MET 3.8 4.5 - - - +
178B LEU* 4.0 36.1 - - + -
201B VAL* 4.3 4.9 - - + +
202B GLY* 1.3 78.7 - - - +
204B CYS* 1.3 61.5 + - - +
207B GLU* 3.4 23.1 - - + +
208B LEU* 4.5 13.0 - - + +
223B LEU* 4.1 19.7 - - + -
240B ARG* 4.3 1.8 - - - +
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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