Contacts of the strand formed by residues 103 - 107 (chain G) in PDB entry 3LUE
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 103 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.6 18.6 - - + +
10G VAL* 5.5 1.1 - - + -
90G PHE* 4.0 29.2 - - + -
98G PRO* 5.6 2.2 - - + +
101G HIS 4.2 2.5 - - - +
102G PRO* 1.3 78.8 - - - +
104G LEU* 1.3 62.1 + - - +
105G LEU* 4.4 12.3 - - + -
123G MET* 3.8 19.1 - - - -
129G THR* 3.8 18.8 - - + -
131G ALA 3.1 4.4 + - - -
132G MET* 3.3 20.7 - - + -
133G TYR 3.1 23.2 + - - +
356G TRP* 3.3 4.6 - - - -
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Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ALA* 5.1 0.4 - - - +
8G LEU 3.2 8.2 + - - +
9G VAL* 3.7 27.4 - - + -
10G VAL* 3.0 26.0 + - - +
102G PRO 4.3 0.4 + - - -
103G VAL* 1.3 73.6 - - - +
105G LEU* 1.3 60.0 + - - +
106G THR* 4.0 9.0 - - + -
133G TYR* 3.4 14.8 - - + +
135G ALA* 4.4 8.1 - - + -
140G LEU* 3.9 24.0 - - + -
343G GLY* 4.1 4.0 - - - +
346G LEU* 3.5 31.4 - - + -
347G ALA* 4.4 12.3 - - + +
352G PHE* 3.5 22.0 - - + -
356G TRP* 4.0 8.8 - - + -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.4 28.9 - - + -
12G ASN* 4.3 3.6 - - - +
86G TRP* 4.4 12.8 - - + -
90G PHE* 5.6 0.4 - - + -
103G VAL* 4.4 9.9 - - + -
104G LEU* 1.3 75.0 - - - +
106G THR* 1.3 68.2 + - - +
119G MET* 3.5 31.9 - - + -
123G MET* 3.8 35.0 - - + -
132G MET* 3.5 27.4 - - + -
133G TYR 2.8 9.2 + - - +
134G VAL* 3.4 19.7 - - + -
135G ALA 3.4 3.1 + - - -
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Residues in contact with THR 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 5.1 2.0 - - + -
10G VAL 2.9 14.2 + - - +
11G ASP* 2.7 33.7 + - + +
12G ASN* 3.4 21.0 + - - +
104G LEU* 4.0 8.3 - - + -
105G LEU* 1.3 79.3 - - - +
107G GLU* 1.3 62.1 - - - +
119G MET* 4.7 4.0 - - - +
134G VAL* 4.4 0.6 - - - +
135G ALA 3.2 9.2 - - - +
137G GLN* 3.8 12.6 + - - +
140G LEU* 3.2 35.0 - - + -
339G VAL* 4.0 9.2 - - + +
340G TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G THR* 1.3 77.1 - - - +
108G ALA* 1.3 68.8 + - - +
111G ASN* 3.1 31.9 + - - +
116G ARG* 3.0 38.3 + - - +
119G MET* 4.4 3.6 - - + -
134G VAL* 3.4 21.5 - - + +
135G ALA 2.7 22.8 + - - +
136G ILE* 3.3 24.5 + - - +
137G GLN* 3.0 33.9 + - - +
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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