Contacts of the strand formed by residues 103 - 108 (chain A) in PDB entry 3LPR
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 ARG 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR 3.7 4.3 - - - -
56A GLY* 3.2 10.3 - - - +
91A ARG* 3.0 3.5 - - - -
93A VAL* 2.8 44.0 + - + -
101A ASN* 3.5 28.0 + - + +
102A ASP* 1.3 73.9 - - - +
104A ALA* 1.3 63.5 + - - +
229A GLU* 2.7 31.2 + - - +
233A PRO* 3.9 37.9 + - - +
234A ILE* 3.7 31.5 - - + +
236A GLN* 2.8 29.6 + - - +
237A TYR* 4.1 18.8 - - + +
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Residues in contact with ALA 104 (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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53A VAL* 3.4 7.6 - - - +
54A THR* 2.9 30.4 + - + +
55A ALA 3.8 10.8 - - - +
56A GLY* 3.9 0.2 - - - -
88A PHE* 3.8 25.1 - - + -
90A ALA 3.2 16.6 - - - +
91A ARG* 3.5 11.2 - - + +
103A ARG* 1.3 79.7 - - - +
105A TRP* 1.3 63.7 + - - +
234A ILE* 4.6 1.9 - - - +
237A TYR* 4.7 7.0 - - - -
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Residues in contact with TRP 105 (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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48A VAL* 3.8 49.3 - + + +
49A THR* 4.0 17.5 - - + -
50A LYS 4.2 4.5 - - - -
51A GLY* 4.2 8.3 - - - -
52A PHE 3.3 10.5 - - - +
53A VAL* 4.2 3.4 - - + -
88A PHE* 3.8 2.3 - - - -
89A ALA* 2.9 40.8 + - + +
90A ALA* 3.2 20.9 + - + +
104A ALA* 1.3 77.0 - - - +
106A VAL* 1.3 77.1 + - - +
107A SER* 3.6 30.5 - - - -
237A TYR* 3.6 37.6 - + + +
239A LEU* 4.0 30.5 - - + -
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Residues in contact with VAL 106 (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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51A GLY* 3.1 23.0 - - - -
52A PHE* 3.0 46.0 + - + +
54A THR* 4.1 4.0 - - + -
66A ALA* 4.0 17.9 - - + -
86A GLY 4.1 1.8 - - - -
87A THR 3.2 29.4 - - - +
88A PHE* 3.8 32.3 - - + -
105A TRP* 1.3 76.9 - - - +
107A SER* 1.3 61.0 + - - +
108A LEU* 3.7 6.5 + - + +
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Residues in contact with SER 107 (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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49A THR* 3.6 16.8 - - - -
50A LYS 3.5 4.5 - - - -
86A GLY* 3.1 2.4 - - - -
87A THR* 2.8 37.2 + - - -
89A ALA* 4.0 10.7 - - - +
105A TRP* 3.6 24.4 - - - -
106A VAL* 1.3 72.6 - - - +
108A LEU* 1.3 63.6 - - - +
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Residues in contact with LEU 108 (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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16A ILE* 4.0 17.3 - - + -
49A THR* 4.8 3.1 - - - +
50A LYS* 2.8 21.2 + - + +
51A GLY* 3.7 21.8 - - - +
52A PHE* 3.9 19.3 - - + -
85A VAL* 3.2 39.3 - - + +
86A GLY* 4.6 0.2 - - - -
106A VAL* 4.0 8.5 - - + +
107A SER* 1.3 78.9 - - - +
109A THR* 1.3 68.8 + - - +
110A SER 3.9 0.3 + - - -
112A GLN* 3.8 11.9 - - + -
114A LEU* 3.6 30.3 - - + -
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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