Contacts of the strand formed by residues 193 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY 3.5 4.2 + - - -
110A THR* 3.4 17.6 - - - +
112A GLY 3.4 7.0 - - - -
113A PRO 4.2 0.2 - - - -
114A SER* 3.5 8.3 - - - -
189A GLN* 3.0 8.1 + - - -
190A THR* 2.8 38.7 + - - +
191A PRO 3.5 0.4 - - - -
192A PHE* 1.3 81.1 - - - +
194A VAL* 1.3 57.5 + - - -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR 4.4 2.5 - - - +
112A GLY 2.9 24.4 + - - +
113A PRO* 3.7 5.4 - - + +
114A SER 3.1 16.2 + - - +
117A GLY* 3.7 9.6 - - - +
187A PRO* 4.9 10.1 - - + -
188A VAL 3.6 10.3 - - - +
189A GLN* 3.5 26.9 - - - +
193A GLY* 1.3 73.7 - - - -
195A VAL* 1.3 71.4 + - - +
196A THR* 4.9 7.9 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 4.7 5.8 - - + -
96A SER* 3.8 24.5 - - - +
114A SER* 3.7 20.9 - - - +
117A GLY 4.0 2.2 - - - -
118A PHE* 4.1 6.1 - - - -
119A GLU* 4.1 15.3 - - + -
187A PRO* 3.3 4.8 - - - +
188A VAL* 3.0 42.6 + - + +
190A THR* 3.8 20.0 - - + -
194A VAL* 1.3 77.4 - - - +
196A THR* 1.3 74.5 + - - +
197A PHE* 4.1 13.1 - - + -
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY 2.8 23.6 + - - +
118A PHE* 3.1 11.6 - - - +
119A GLU 3.1 23.0 + - - -
187A PRO* 4.2 22.9 - - + -
194A VAL* 4.9 9.0 - - + -
195A VAL* 1.3 79.3 - - - +
197A PHE* 1.3 65.6 + - - +
198A LEU* 5.1 5.5 - - - +
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.9 25.6 - - + -
40A GLU* 4.4 5.8 - - + -
91A ILE* 5.1 1.3 - - + -
119A GLU* 3.5 17.0 - - + -
121A THR* 4.2 10.3 - - + -
181A GLU* 3.7 5.7 - - - +
182A ASP* 3.0 30.6 + - + -
185A MET* 3.4 57.8 + - + +
186A GLN 3.2 27.8 - - - -
187A PRO* 4.4 2.1 - - - +
188A VAL* 4.1 20.0 - - + -
195A VAL* 4.1 21.5 - - + -
196A THR* 1.3 79.3 - - - +
198A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.7 34.5 - - + -
119A GLU 3.1 10.2 + - - +
120A LEU* 3.4 13.7 - - + +
121A THR* 2.9 24.7 + - - +
155A PHE* 3.4 37.0 - - + +
156A CYS* 3.9 3.1 - - - +
157A SER* 3.6 33.0 - - - +
179A LEU* 4.6 9.4 - - + -
180A THR 3.3 13.7 - - - +
181A GLU* 4.7 2.7 - - + +
196A THR* 4.1 6.0 + - - +
197A PHE* 1.3 72.4 - - - +
199A GLN* 1.3 61.3 + - - +
200A ILE 3.7 0.5 + - - -
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 3.3 25.1 + - - +
122A PHE* 4.3 2.7 - - - -
123A ARG* 3.2 24.9 + - + +
179A LEU* 3.5 7.1 - - - -
180A THR* 2.6 43.3 + - + +
182A ASP* 3.7 7.7 - - - +
183A PRO* 3.1 27.4 - - - +
197A PHE 3.8 1.0 + - - -
198A LEU* 1.3 70.4 - - - +
200A ILE* 1.3 72.1 + - - +
201A VAL* 3.5 10.8 + - - +
233A TRP 3.3 7.8 + - - +
234A LEU* 2.7 37.6 + - - +
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.0 14.1 - - + -
121A THR 2.8 17.3 + - - +
122A PHE* 3.4 35.2 - - + -
123A ARG 4.6 0.5 + - - -
140A LEU* 4.7 10.5 - - + -
141A MET* 3.9 27.8 - - + -
144A LEU* 3.8 22.2 - - + -
167A LEU* 5.3 0.4 - - + -
177A MET* 3.6 33.0 - - + -
178A LEU 3.7 4.0 - - - -
179A LEU* 3.9 16.6 - - + -
198A LEU 3.7 0.4 + - - -
199A GLN* 1.3 81.8 + - - +
201A VAL* 1.3 66.8 + - - +
236A THR* 4.3 1.6 + - - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A MET* 3.2 5.2 - - - -
178A LEU* 2.8 48.7 + - + +
180A THR* 3.8 11.2 - - + -
199A GLN* 3.6 17.9 - - - +
200A ILE* 1.3 79.9 - - - +
202A GLY* 1.3 68.6 + - - +
203A VAL* 3.7 1.4 + - + +
220A LEU* 4.5 4.3 - - + -
223A LEU* 4.4 22.2 - - + -
229A ALA 5.8 0.9 - - - +
230A GLY 5.6 5.4 - - - +
234A LEU* 3.7 40.2 - - + +
236A THR* 3.9 5.2 - - - +
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 4.7 2.4 - - - -
167A LEU* 3.9 7.9 - - - -
174A ILE* 3.6 27.3 - - - +
176A HIS 3.3 9.4 - - - -
200A ILE 4.2 0.2 - - - -
201A VAL* 1.3 76.8 - - - +
203A VAL* 1.3 64.6 + - - +
223A LEU* 5.7 0.3 - - - +
229A ALA 4.5 5.4 - - - +
236A THR* 3.1 24.0 + - - +
240A ARG* 3.9 5.0 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.6 3.9 - - - +
175A GLN 3.0 8.6 + - - -
176A HIS* 2.8 55.6 + - + -
177A MET* 3.7 14.1 - - - +
178A LEU* 4.1 17.3 - - + +
201A VAL* 4.3 4.3 - - + +
202A GLY* 1.3 79.3 - - - +
204A CYS* 1.3 66.4 + - - +
207A GLU* 3.4 26.5 - - + +
208A LEU* 4.5 9.0 - - + +
223A LEU* 4.1 26.7 - - + -
240A ARG* 4.2 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