Contacts of the strand formed by residues 113 - 117 (chain A) in PDB entry 2LBP
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 HIS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLU* 4.1 29.4 + - + +
93A GLY* 3.3 41.4 + - - -
94A ILE 3.6 12.8 - - - +
95A LEU* 3.8 13.4 - - + +
96A MET 3.2 22.9 + - - +
111A TYR 3.4 0.4 - - - -
112A GLN* 1.3 85.5 - - + +
114A ILE* 1.3 64.4 + - + +
115A MET* 4.2 1.6 - - - -
299A PRO* 4.0 16.5 - - + +
300A LEU* 3.7 33.8 - - + +
303A VAL* 4.9 2.2 - - - -
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 3.7 41.1 - - - +
89A TYR* 4.4 1.3 - - + -
90A GLU* 4.1 20.4 - - + +
96A MET* 3.3 24.0 - - + -
106A LEU* 3.9 40.6 - - + +
107A THR* 4.7 7.2 - - - +
111A TYR* 4.1 17.8 + - + +
112A GLN 3.7 1.8 - - - -
113A HIS* 1.3 89.2 - - + +
115A MET* 1.3 67.5 + - - +
116A ARG* 5.9 0.2 - - + -
307A LYS* 4.7 3.3 + - - -
323A LYS 3.9 5.7 - - - +
324A GLY* 3.8 13.9 - - - +
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.9 17.7 - - + -
96A MET* 2.7 15.7 + - - +
97A ILE* 3.4 18.3 - - + -
98A SER* 3.0 23.2 + - - -
114A ILE* 1.3 80.2 - - - +
116A ARG* 1.3 67.5 + - - +
302A LEU 4.2 0.4 - - - +
303A VAL* 3.4 50.3 - - + +
306A LEU* 3.7 35.0 - - + -
307A LYS* 4.8 4.7 - - - -
320A TRP* 4.6 23.3 - - + +
324A GLY* 3.5 13.0 - - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.3 1.6 - - - -
98A SER* 3.5 11.9 - - - +
101A ALA 3.3 19.1 + - - +
102A THR 3.3 2.6 - - - -
103A ALA* 2.2 49.9 + - - +
104A PRO 3.8 7.7 + - - -
106A LEU* 3.5 30.7 - - + +
107A THR* 3.5 12.1 + - - +
114A ILE* 5.9 0.4 - - + -
115A MET* 1.3 81.8 - - - +
117A THR* 1.3 61.4 - - - +
118A ALA 3.4 13.7 - - - +
120A LEU* 3.4 32.0 - - - +
320A TRP* 2.7 31.2 + - - -
324A GLY 3.2 8.3 + - - +
325A ASP* 2.9 40.0 + - - +
326A LEU* 3.6 6.8 - - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.1 9.2 - - + -
98A SER 3.1 10.7 + - - -
99A PRO* 3.8 3.3 - - - +
116A ARG* 1.3 75.3 - - - +
118A ALA* 1.3 59.2 + - - +
119A GLY 4.2 0.5 + - - -
279A ILE* 2.8 31.4 + - - +
282A ALA* 4.1 10.5 - - - +
283A ALA* 3.6 31.5 - - - +
286A SER* 4.4 1.1 - - - +
315A ILE* 3.7 17.2 - - - +
318A LEU* 4.2 9.2 - - + -
320A TRP* 4.1 18.4 - - + -
326A LEU* 3.7 17.4 - - - +
329A PHE* 4.7 1.6 - - - -
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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