Contacts of the strand formed by residues 190 - 196 (chain A) in PDB entry 3PE7
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 LEU 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.9 3.3 - - - -
142A ILE* 3.6 28.3 - - + +
168A CYS* 3.6 31.8 - - + +
170A LEU* 4.8 11.4 - - + +
184A LEU* 3.9 26.5 - - + -
186A GLU* 3.8 20.4 - - + +
188A GLN* 3.1 15.9 + - + +
189A TRP* 1.3 90.8 - - - +
191A GLY* 1.3 58.8 + - - +
205A PHE* 3.9 15.3 - - + -
206A CYS 3.4 1.3 - - - +
207A HIS* 3.7 28.9 - - + -
208A GLU* 4.7 0.4 - - - -
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Residues in contact with GLY 191 (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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127A TYR* 4.2 12.1 - - - -
142A ILE* 4.0 6.2 - - - +
189A TRP 4.2 0.2 + - - -
190A LEU* 1.3 76.4 - - - +
192A HIS* 1.3 66.0 + - - -
193A PRO* 3.2 6.8 - - - +
205A PHE* 3.6 3.8 - - - +
206A CYS* 2.8 44.5 + - - -
208A GLU* 4.7 3.8 - - - -
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Residues in contact with HIS 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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38A PHE* 6.3 0.9 - + - -
39A TYR* 4.1 36.5 - + - -
127A TYR* 5.1 3.4 - - - -
129A THR* 5.8 3.1 - - - +
131A VAL* 5.6 0.9 - - + -
142A ILE* 4.6 0.6 - - - +
191A GLY* 1.3 72.4 - - - +
193A PRO* 1.3 71.6 - - - +
194A ILE* 3.5 38.2 + - + +
204A ALA 3.6 0.5 - - - +
205A PHE* 3.6 9.9 - - - -
206A CYS* 4.0 13.4 - - + -
208A GLU* 5.9 0.2 - - - +
217A ARG* 5.0 1.3 + - - +
243A GLU* 2.9 45.6 + - - +
244A PHE* 4.9 2.2 - - + -
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Residues in contact with PRO 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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127A TYR 5.8 1.1 - - - +
129A THR 4.6 8.8 - - - +
131A VAL* 3.7 16.3 - - - +
140A VAL* 3.8 17.6 - - + +
141A GLY* 3.6 34.8 - - - +
142A ILE* 3.6 16.4 - - + +
170A LEU* 4.2 18.4 - - + -
191A GLY 3.2 5.3 - - - -
192A HIS* 1.3 88.3 - - - +
194A ILE* 1.3 65.3 + - - +
203A VAL* 4.4 1.6 - - + -
204A ALA 3.2 9.9 - - - +
205A PHE* 4.0 5.8 - - + -
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Residues in contact with ILE 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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39A TYR* 4.7 7.2 - - + -
131A VAL* 3.8 22.4 - - + -
140A VAL* 4.1 0.8 - - - +
192A HIS* 3.6 45.8 - - + +
193A PRO* 1.3 79.5 - - - +
195A TYR* 1.3 66.0 + - - +
203A VAL* 4.2 3.1 - - - +
204A ALA* 2.8 49.9 + - + +
243A GLU* 4.7 4.0 - - + +
244A PHE* 4.4 3.1 - - - -
245A TRP* 3.0 40.6 + - + +
252A LEU* 4.3 10.8 - - + -
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Residues in contact with TYR 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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131A VAL* 4.0 6.5 - - - +
132A ALA 3.9 15.9 - - - +
133A ASN* 3.5 28.9 - - + -
138A LYS* 3.5 32.8 - - + +
139A LEU 4.0 6.1 - - - -
140A VAL* 3.7 37.2 - - + +
172A ARG* 3.7 12.3 - - - +
194A ILE* 1.3 73.6 - - - +
196A ARG* 1.3 65.6 + - - +
197A PRO* 3.3 4.3 - - - +
200A ASP* 3.3 42.6 - - + -
202A THR 3.9 3.8 - - - -
203A VAL* 4.0 15.9 - - + +
223A GLU* 2.7 23.1 + - + +
245A TRP* 3.3 11.1 - - - -
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Residues in contact with ARG 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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134A SER 5.4 1.4 + - - -
194A ILE 3.5 2.4 + - - -
195A TYR* 1.3 74.0 - - - +
197A PRO* 1.4 82.0 + - + +
198A TYR 3.2 0.7 + - - -
199A ASP* 3.1 51.2 + - + +
200A ASP* 4.8 1.4 - - - +
202A THR* 2.9 27.0 + - - +
245A TRP* 3.5 34.1 - - + +
249A GLY 2.8 26.6 + - - +
250A SER* 4.3 4.9 + - - +
271A PRO* 3.6 22.9 - - - +
272A GLU* 2.7 39.6 + - - +
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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