Contacts of the strand formed by residues 120 - 125 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E CYS* 3.3 39.3 - - + -
86E LEU* 3.8 21.5 - - + -
103E ARG* 3.7 45.3 - - + -
106E PHE* 3.2 27.4 - + - -
107E LEU* 3.8 23.3 - - + -
115E PRO 4.9 0.4 - - - -
118E PHE* 3.1 24.7 + + + -
119E PRO* 1.3 77.2 - - - +
121E VAL* 1.3 68.7 + - - +
149E ILE* 3.6 31.0 - - + +
150E PRO* 3.4 18.7 - - - +
172E ASN* 4.6 0.7 + - - -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E CYS* 4.4 7.2 - - - -
84E CYS 2.9 8.1 + - - +
85E VAL* 3.4 3.1 - - - +
86E LEU* 2.8 32.8 + - - +
120E PHE* 1.3 81.0 - - - +
122E VAL* 1.3 70.4 + - - +
123E LEU* 4.0 5.4 - - + -
149E ILE* 5.3 0.2 - - - -
150E PRO* 3.9 19.7 - - + +
152E PHE* 4.0 23.8 - - + -
168E THR* 4.8 2.5 - - + -
169E ILE* 3.5 48.7 - - + +
172E ASN* 4.5 7.4 - - - +
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Residues in contact with VAL 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LEU* 3.2 16.8 - - + +
88E PHE* 3.7 23.8 - - + -
96E PHE* 6.2 0.2 - - + -
99E LEU* 4.1 8.3 - - + -
121E VAL* 1.3 78.5 - - - +
123E LEU* 1.3 67.9 + - - +
139E ALA* 5.8 0.4 - - + -
142E TRP* 3.7 28.3 - - + -
143E CYS* 3.7 20.4 - - - -
149E ILE* 4.0 10.8 - - + -
150E PRO 3.2 5.6 + - - +
151E TYR* 3.5 19.4 - - + -
152E PHE 3.1 24.8 + - - +
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 3.7 22.7 - - + -
85E VAL* 3.7 27.1 - - + -
86E LEU 2.7 12.2 + - - +
87E VAL* 3.6 10.0 - - + +
88E PHE* 3.2 31.3 + - - -
121E VAL* 4.0 10.3 - - + -
122E VAL* 1.3 83.9 - - - +
124E GLY* 1.3 60.7 + - - +
125E ASN 3.5 2.0 + - - -
152E PHE* 3.4 23.8 - - + -
154E THR* 4.1 16.8 - - + +
165E ALA* 3.8 20.4 - - + -
166E PHE* 4.7 13.7 - - + -
169E ILE* 4.8 2.5 - - + -
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Residues in contact with GLY 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PHE* 3.5 27.2 - - - -
90E VAL* 3.8 6.7 - - - -
123E LEU* 1.3 69.3 - - - +
125E ASN* 1.3 56.7 + - - -
127E ILE* 3.8 3.5 - - - +
151E TYR* 4.0 8.2 - - - -
152E PHE 2.5 15.6 + - - -
153E GLU* 3.0 7.6 - - - +
154E THR* 2.6 29.9 + - - +
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Residues in contact with ASN 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL 3.1 19.2 - - - +
20E GLY* 4.1 2.4 - - - -
24E LEU* 3.0 26.7 - - - +
87E VAL* 3.8 15.7 - - + -
88E PHE 2.8 19.0 + - - +
89E ASP* 3.7 0.2 - - - -
90E VAL* 3.1 24.4 + - - +
123E LEU 3.5 0.2 + - - -
124E GLY* 1.3 74.5 - - - +
126E LYS* 1.3 72.1 + - - +
154E THR* 2.6 36.5 + - - +
156E ALA 3.5 5.3 - - - +
1400E GNP 3.3 22.2 + - - +
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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