Contacts of the strand formed by residues 103 - 107 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.6 17.3 - - + +
10H VAL* 5.5 1.8 - - + -
90H PHE* 4.0 29.2 - - + -
98H PRO* 5.6 2.7 - - + +
101H HIS* 4.2 2.9 - - + +
102H PRO* 1.3 78.8 - - - +
104H LEU* 1.3 62.7 + - - +
105H LEU* 4.4 12.3 - - + -
123H MET* 3.8 19.5 - - - -
129H THR* 3.8 18.2 - - + -
131H ALA 3.1 4.6 + - - -
132H MET* 3.3 19.7 - - + -
133H TYR 3.1 22.7 + - - +
356H TRP* 3.3 4.9 - - - -
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Residues in contact with LEU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ALA* 5.1 0.4 - - + +
8H LEU 3.2 8.4 + - - +
9H VAL* 3.7 26.6 - - + -
10H VAL* 3.0 25.3 + - - +
103H VAL* 1.3 74.1 - - - +
105H LEU* 1.3 61.5 + - - +
106H THR* 4.0 8.5 - - + -
133H TYR* 3.4 14.8 - - + +
135H ALA* 4.4 7.6 - - + -
140H LEU* 3.9 23.8 - - + -
343H GLY* 4.1 3.8 - - - +
346H LEU* 3.5 31.6 - - + -
347H ALA* 4.4 12.3 - - + +
352H PHE* 3.5 21.3 - - + -
356H TRP* 4.0 9.9 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H VAL* 3.4 29.4 - - + -
12H ASN* 4.3 3.4 - - - +
86H TRP* 4.4 13.0 - - + -
90H PHE* 5.6 0.4 - - + -
103H VAL* 4.4 9.6 - - + -
104H LEU* 1.3 75.0 - - - +
106H THR* 1.3 66.6 + - - +
119H MET* 3.5 32.5 - - + -
123H MET* 3.8 33.7 - - + -
132H MET* 3.5 27.4 - - + -
133H TYR 2.8 8.6 + - - +
134H VAL* 3.4 19.5 - - + +
135H ALA 3.4 3.1 + - - -
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Residues in contact with THR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 5.1 2.0 - - + -
10H VAL 2.9 13.5 + - - +
11H ASP* 2.7 33.5 + - + +
12H ASN* 3.4 20.7 + - - +
104H LEU* 4.0 9.0 - - + -
105H LEU* 1.3 78.9 - - - +
107H GLU* 1.3 63.2 + - - +
119H MET* 4.7 4.2 - - - +
134H VAL* 4.4 0.7 - - - +
135H ALA 3.2 9.6 - - - +
137H GLN* 3.8 13.4 + - - +
140H LEU* 3.2 35.0 - - + -
339H VAL* 4.0 9.6 - - + +
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H THR* 1.3 76.8 - - - +
108H ALA* 1.3 67.3 + - - +
111H ASN* 3.1 32.6 + - - +
116H ARG* 3.0 39.1 + - - +
119H MET* 4.4 4.0 - - + -
134H VAL* 3.4 21.2 - - + +
135H ALA 2.7 22.8 + - - +
136H ILE* 3.3 24.4 + - - +
137H GLN* 3.0 33.5 + - - +
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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