Contacts of the strand formed by residues 120 - 125 (chain D) in PDB entry 3LAW
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 PHE 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D CYS* 4.5 0.2 - - - -
84D CYS* 3.2 31.0 - - + +
86D LEU* 4.1 15.0 - - + -
103D ARG* 3.8 47.6 - - + -
106D PHE* 3.5 23.8 - + - -
107D LEU* 3.6 33.7 - - + -
115D PRO 4.2 2.5 - - - -
118D PHE* 3.1 37.0 + + - -
119D PRO* 1.3 77.1 - - - +
121D VAL* 1.3 73.8 + - - +
149D ILE* 4.0 28.5 - - + +
150D PRO* 3.4 17.2 - - - +
172D ASN* 4.9 0.7 + - - -
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Residues in contact with VAL 121 (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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83D CYS* 3.9 12.8 - - - -
84D CYS 3.0 7.5 + - - +
85D VAL* 3.3 5.1 - - - +
86D LEU* 2.7 33.3 + - - +
120D PHE* 1.3 85.4 - - - +
122D VAL* 1.3 59.9 + - - +
123D LEU* 3.8 23.1 - - + -
149D ILE* 5.3 0.2 - - - -
150D PRO* 3.6 26.2 - - + +
152D PHE* 4.0 16.2 - - + -
168D THR 4.8 1.3 - - - +
169D ILE* 3.6 40.8 - - + +
172D ASN* 5.1 2.7 - - - +
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Residues in contact with VAL 122 (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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86D LEU* 3.1 20.9 - - + +
88D PHE* 3.7 24.7 - - + -
96D PHE* 6.0 0.2 - - + -
99D LEU* 4.0 6.7 - - + -
121D VAL* 1.3 75.2 - - - +
123D LEU* 1.3 69.0 + - - +
142D TRP* 3.8 13.9 - - + -
143D CYS* 3.6 27.1 - - - -
149D ILE* 3.7 18.2 - - + -
150D PRO 3.0 6.9 + - - +
151D TYR* 3.5 19.5 - - + -
152D PHE 3.0 24.1 + - - -
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Residues in contact with LEU 123 (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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24D LEU* 4.0 26.7 - - + -
85D VAL* 3.5 28.7 - - + -
86D LEU 2.7 11.1 + - - +
87D VAL* 3.6 8.9 - - + +
88D PHE* 3.0 29.1 + - - -
121D VAL* 3.8 18.6 - - + -
122D VAL* 1.3 86.5 - - - +
124D GLY* 1.3 59.6 + - - +
125D ASN 3.3 1.9 + - - -
152D PHE* 3.2 13.7 - - + +
154D THR* 4.1 12.6 - - + +
165D ALA* 3.8 27.4 - - + -
166D PHE* 4.9 12.3 - - + -
169D ILE* 5.0 1.3 - - + -
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Residues in contact with GLY 124 (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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88D PHE* 3.6 28.7 - - - -
90D VAL* 3.7 5.7 - - - +
123D LEU* 1.3 67.4 - - - +
125D ASN* 1.3 61.6 + - - -
127D ILE* 3.7 6.1 - - - +
151D TYR* 3.7 14.0 - - - -
152D PHE 2.8 11.8 + - - -
153D GLU* 3.1 10.2 - - - +
154D THR 3.0 19.4 + - - -
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Residues in contact with ASN 125 (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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19D VAL 3.0 23.4 - - - +
20D GLY* 3.9 4.3 - - - -
24D LEU* 3.8 21.9 - - + +
87D VAL* 4.2 4.0 - - + -
88D PHE 2.8 16.5 + - - +
89D ASP* 3.6 1.6 - - - -
90D VAL* 3.0 23.0 + - - +
123D LEU 3.3 0.9 + - - +
124D GLY* 1.3 74.6 - - - +
126D LYS* 1.3 88.6 + - - +
154D THR* 2.9 31.0 + - - +
156D ALA 3.3 10.7 - - - +
1400D GNP 3.2 28.7 + - - +
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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