Contacts of the strand formed by residues 103 - 107 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.6 17.9 - - + +
10I VAL* 5.5 1.3 - - + -
90I PHE* 4.0 29.4 - - + -
98I PRO* 5.6 2.2 - - + +
101I HIS 4.2 2.7 - - - +
102I PRO* 1.3 78.4 - - - +
104I LEU* 1.3 63.7 + - - +
105I LEU* 4.4 13.2 - - + -
123I MET* 3.8 19.1 - - - -
129I THR* 3.8 19.1 - - + -
131I ALA 3.1 4.2 + - - -
132I MET* 3.3 20.5 - - + -
133I TYR 3.1 22.9 + - - +
356I TRP* 3.3 5.1 - - - -
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Residues in contact with LEU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LEU 3.2 8.8 + - - +
9I VAL* 3.7 27.9 - - + -
10I VAL* 3.0 24.9 + - - +
103I VAL* 1.3 74.6 - - - +
105I LEU* 1.3 61.6 + - - +
106I THR* 4.0 7.6 - - + -
133I TYR* 3.4 14.8 - - + +
135I ALA* 4.4 8.7 - - + -
140I LEU* 3.9 23.6 - - + -
343I GLY* 4.1 3.6 - - - +
346I LEU* 3.5 31.2 - - + -
347I ALA* 4.4 12.6 - - + +
352I PHE* 3.5 21.8 - - + -
356I TRP* 4.0 10.1 - - + -
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Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 3.4 28.9 - - + -
12I ASN* 4.3 2.9 - - - +
86I TRP* 4.4 13.2 - - + +
90I PHE* 5.6 0.2 - - + -
103I VAL* 4.4 10.1 - - + -
104I LEU* 1.3 74.1 - - - +
106I THR* 1.3 67.6 + - - +
119I MET* 3.5 32.3 - - + -
123I MET* 3.8 33.4 - - + -
132I MET* 3.5 27.4 - - + -
133I TYR 2.8 9.1 + - - +
134I VAL* 3.4 20.1 - - + +
135I ALA 3.4 3.3 + - - -
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Residues in contact with THR 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 5.1 2.2 - - + -
10I VAL 2.9 13.6 + - - +
11I ASP* 2.7 33.0 + - + +
12I ASN* 3.4 20.0 + - - +
104I LEU* 4.0 8.5 - - + -
105I LEU* 1.3 79.7 - - - +
107I GLU* 1.3 63.5 + - - +
119I MET* 4.7 4.0 - - - +
134I VAL* 4.6 0.7 - - - +
135I ALA 3.2 9.4 - - - +
137I GLN* 3.8 13.1 + - - +
140I LEU* 3.2 34.8 - - + -
339I VAL* 4.0 9.4 - - + +
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Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I THR* 1.3 77.7 - - - +
108I ALA* 1.3 69.3 + - - +
111I ASN* 3.1 31.7 + - - +
116I ARG* 3.0 39.1 + - - +
119I MET* 4.4 4.0 - - + -
134I VAL* 3.4 21.1 - - + +
135I ALA 2.7 21.8 + - - +
136I ILE* 3.3 24.0 + - - +
137I GLN* 3.0 33.1 + - - +
374I CYS 5.4 0.2 - - - +
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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