Contacts of the strand formed by residues 189 - 199 (chain A) in PDB entry 3ICU
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 VAL 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.5 31.0 - - + -
50A SER 3.3 5.2 - - - +
51A TRP* 3.6 33.2 - - + +
83A VAL* 3.6 4.4 - - - +
84A LEU* 2.8 42.7 + - + +
179A ILE* 4.1 11.4 - - + +
182A SER* 4.0 10.1 - - - -
183A ILE* 4.0 17.7 - - + +
187A ILE 3.5 11.1 + - - +
188A GLN* 1.3 77.7 - - - +
190A THR* 1.3 63.6 + - - +
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Residues in contact with THR 190 (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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48A ASN 3.8 1.3 - - - +
49A VAL* 3.4 5.0 - - - +
50A SER* 2.8 44.1 + - - -
81A ALA* 5.7 2.0 - - + -
82A GLY* 3.5 20.4 - - - +
83A VAL* 4.0 15.7 - - + +
188A GLN* 4.4 10.6 + - - +
189A VAL* 1.3 76.4 - - - +
191A MET* 1.3 68.1 + - - +
192A VAL* 5.3 7.0 - - + -
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Residues in contact with MET 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.1 22.4 - - + -
48A ASN 3.5 2.9 - - - -
49A VAL* 3.6 28.9 - - + -
81A ALA* 3.2 3.1 - - - +
82A GLY 2.9 32.4 + - - -
84A LEU* 3.8 16.4 - - + +
117A LEU* 3.6 9.7 - - + +
144A VAL* 3.9 32.5 - - + -
169A ILE* 4.3 1.3 - - - -
171A ILE* 4.7 2.7 - - + -
175A LYS* 5.7 0.4 - - - -
179A ILE* 4.0 19.3 - - + -
189A VAL 4.3 0.2 + - - -
190A THR* 1.3 76.5 - - - +
192A VAL* 1.3 68.6 + - - +
193A ILE* 3.7 27.8 - - + -
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Residues in contact with VAL 192 (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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46A TYR 3.6 1.2 - - - +
47A LEU* 3.5 4.0 - - - -
48A ASN* 2.9 50.3 + - + +
79A PRO* 5.9 1.1 - - + -
80A VAL 3.6 8.1 - - - +
81A ALA* 4.0 17.5 - - + -
190A THR* 5.3 6.3 - - + -
191A MET* 1.3 76.3 - - - +
193A ILE* 1.3 63.4 + - - +
194A GLU* 3.7 27.6 - - + +
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Residues in contact with ILE 193 (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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45A ALA* 4.0 10.8 - - + -
46A TYR 3.5 2.9 - - - -
47A LEU* 4.0 4.7 - - + -
71A TYR* 3.5 24.5 - - + +
79A PRO* 3.1 7.8 - - - +
80A VAL* 2.7 58.8 + - + +
117A LEU* 4.1 8.1 - - + -
142A GLY* 6.0 0.9 - - - -
143A ALA 5.5 0.9 - - - +
144A VAL* 3.9 12.6 - - + -
167A VAL* 4.5 6.1 - - + -
169A ILE* 3.8 33.7 - - + -
191A MET* 3.7 28.3 - - + -
192A VAL* 1.3 74.1 - - - +
194A GLU* 1.3 66.4 + - - +
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Residues in contact with GLU 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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45A ALA* 3.4 6.8 - - - -
46A TYR* 2.9 47.0 + - + +
65A LEU* 6.1 0.5 - - - +
71A TYR* 3.3 8.3 - - - -
79A PRO* 3.8 18.1 - - + +
192A VAL* 3.7 21.3 - - + +
193A ILE* 1.3 78.5 - - - +
195A VAL* 1.3 64.0 - - - +
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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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43A TRP* 3.6 31.2 - - + -
44A THR 5.0 0.2 - - - +
46A TYR* 3.5 11.6 - - - -
71A TYR* 3.7 13.0 - - + +
77A LEU* 3.6 24.2 - - + +
78A GLU* 3.5 32.9 - - - +
79A PRO* 4.6 3.5 - - + +
194A GLU* 1.3 74.1 - - - +
196A GLY* 1.3 64.9 + - - +
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Residues in contact with GLY 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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43A TRP* 3.8 13.8 - - - -
44A THR* 2.8 27.3 + - - -
45A ALA 4.5 0.2 - - - -
46A TYR* 3.6 23.2 - - - -
194A GLU 3.4 1.6 + - - -
195A VAL* 1.3 77.8 - - - +
197A LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 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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42A VAL 3.6 1.0 - - - +
43A TRP* 3.3 8.0 - - - -
44A THR* 2.8 30.2 + - - -
46A TYR* 3.4 23.5 + - + +
67A GLU* 3.7 25.4 + - - +
196A GLY* 1.3 77.6 - - - +
198A LYS* 1.3 64.5 + - - +
199A HIS* 3.7 14.2 + - + +
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Residues in contact with LYS 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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41A ALA* 3.6 26.2 - - + -
42A VAL 3.8 3.1 - - - -
43A TRP* 3.7 43.2 - - + +
197A LYS* 1.3 74.2 - - - +
199A HIS* 1.3 67.7 + - - +
200A GLY 3.7 17.2 + - - +
201A PRO* 4.7 6.6 - - - +
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Residues in contact with HIS 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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38A GLY* 5.4 1.3 - - - -
40A GLU 4.0 2.1 - - - +
41A ALA* 3.3 1.0 - - - -
42A VAL* 2.8 45.6 + - + +
44A THR* 3.6 31.4 - - + +
67A GLU* 4.5 3.4 - - - -
197A LYS* 3.7 20.0 + - + +
198A LYS* 1.3 74.4 + - - +
200A GLY* 1.3 64.1 + - - +
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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