Contacts of the strand formed by residues 187 - 193 (chain D) in PDB entry 3AB0
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 SER 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D VAL* 3.6 2.8 - - - +
128D ILE* 2.7 41.8 + - - +
155D VAL* 4.3 1.6 - - - -
156D ASN* 3.4 25.3 + - - -
182D ILE* 3.5 32.3 - - - +
184D THR* 2.5 26.1 + - - +
186D PRO* 1.3 71.9 + - - +
188D LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 4.2 14.6 - - + -
126D PHE 3.3 3.6 - - - +
127D VAL* 4.3 22.2 - - + -
154D GLN 3.6 0.6 - - - +
155D VAL* 3.1 9.9 - - - +
156D ASN* 2.9 35.8 + - - +
186D PRO* 5.4 5.8 - - + +
187D SER* 1.3 81.0 - - - +
189D VAL* 1.3 61.6 + - - +
190D GLU* 5.4 2.7 - - + +
101E TRP* 4.2 15.5 - - + +
91F TYR* 3.7 40.8 - - + +
92F HIS* 3.9 27.8 - - + +
94F TYR* 5.5 11.0 - - + -
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 4.0 0.2 - - - -
126D PHE* 2.7 54.2 + - + +
128D ILE* 3.6 33.7 - - + -
136D ILE* 3.9 22.2 - - + -
153D ILE* 4.6 9.6 - - + -
154D GLN 3.6 4.5 - - - +
155D VAL* 3.9 17.5 - - + -
182D ILE* 5.4 0.2 - - + -
187D SER 5.1 0.7 - - - +
188D LEU* 1.3 79.2 - - - +
190D GLU* 1.3 65.9 + - - +
208D ILE* 4.7 11.4 - - + -
210D ILE* 4.2 15.7 - - + -
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PRO* 5.2 0.2 - - + -
124D ASP 3.7 17.5 - - - +
125D THR* 4.1 18.7 + - + +
126D PHE* 5.3 2.9 - - - -
153D ILE* 3.7 2.6 - - - +
154D GLN* 2.8 61.8 + - + +
157D GLY* 4.2 2.2 - - - +
188D LEU* 5.3 3.1 - - + +
189D VAL* 1.3 80.2 - - - +
191D VAL* 1.3 62.5 + - - +
192D ILE* 3.8 9.4 - - + +
32F TYR* 4.7 0.7 - - - -
50F ARG* 3.5 20.5 + - - -
91F TYR* 4.1 1.9 + - - -
92F HIS* 2.7 42.4 + - - -
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PRO* 3.2 4.9 - - - +
105D VAL* 2.9 37.1 + - + +
107D PHE* 3.8 30.2 - - + -
124D ASP 5.1 1.4 + - - -
126D PHE* 6.4 0.4 - - + -
138D VAL* 4.0 27.4 - - + -
151D LEU* 3.8 30.7 - - + -
152D THR 3.3 15.5 - - - +
153D ILE* 4.5 10.5 - - + -
176D ILE* 5.5 0.7 - - + -
189D VAL* 5.7 0.2 - - + -
190D GLU* 1.3 77.3 - - - +
192D ILE* 1.3 62.2 + - - +
208D ILE* 4.1 9.6 - - + -
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C THR* 6.1 0.2 - - - +
102D ASN* 3.5 30.5 - - - +
103D ASP 3.7 0.4 - - - -
104D PRO* 3.8 14.1 - - + -
151D LEU* 3.5 5.5 - - - -
152D THR* 2.7 41.4 + - - +
154D GLN* 3.4 35.2 - - + +
190D GLU* 3.8 12.3 - - + +
191D VAL* 1.3 80.9 - - - +
193D VAL* 1.3 77.0 + - - +
194D THR* 3.5 4.4 + - + -
32F TYR* 4.1 9.2 - - + +
50F ARG* 3.8 26.5 - - - +
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 3.8 32.5 - - + -
100D GLY 3.4 20.0 - - - +
101D ILE* 4.6 0.2 - - - -
102D ASN* 2.9 29.6 + - - +
103D ASP 2.9 24.6 + - - +
105D VAL* 4.2 10.3 - - + -
150D GLY 3.6 4.9 - - - +
151D LEU* 4.1 5.8 - - + -
192D ILE* 1.3 75.2 - - - +
194D THR* 1.3 65.8 + - - +
197D GLY* 3.6 9.6 - - - -
198D LEU* 3.6 32.5 - - + +
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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