Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 3LON
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 ASP 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 3.0 10.4 + - - +
102A SER* 1.3 77.8 + - - +
104A LEU* 1.3 64.1 + - - +
105A TYR* 4.0 13.6 - - - +
116A VAL 4.1 2.7 - - - -
117A ARG* 3.4 24.1 + - - +
145A CYS* 3.9 0.3 - - - -
146A PRO* 3.2 36.0 - - + +
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Residues in contact with LEU 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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101A SER 3.6 23.6 - - - +
102A SER* 3.9 8.7 - - - +
103A ASP* 1.3 77.7 - - - +
105A TYR* 1.3 71.7 + - - +
106A LEU 4.3 0.2 - - - -
115A PRO* 3.4 2.9 - - - +
116A VAL* 2.8 54.2 + - + +
118A ARG* 4.0 23.3 - - + +
143A LEU* 4.1 17.5 - - + -
144A LEU 3.2 7.2 - - - +
145A CYS* 4.6 1.8 - - - -
151A VAL* 3.7 42.4 - - + -
169A PHE* 4.2 7.0 - - + -
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Residues in contact with TYR 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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3A ILE* 3.6 28.3 - - + -
103A ASP* 4.0 25.6 - - + +
104A LEU* 1.3 78.8 - - - +
106A LEU* 1.3 62.0 + - - +
107A VAL* 3.8 0.7 + - - +
113A VAL* 3.9 15.0 - - + -
114A ILE 3.3 3.4 - - - -
115A PRO* 3.7 26.9 - - + -
142A PRO 3.7 1.4 - - - +
143A LEU* 3.4 2.7 - - - -
144A LEU* 2.8 46.0 + - + +
145A CYS 4.3 1.8 - - - -
146A PRO* 4.1 11.9 - - + +
99C CYS* 3.8 20.1 - - - +
101C SER* 4.5 2.6 - - - -
146C PRO* 3.5 32.1 - - + +
147C ALA* 3.5 30.1 - - + -
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Residues in contact with LEU 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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104A LEU 4.3 0.4 - - - -
105A TYR* 1.3 70.7 - - - +
107A VAL* 1.3 77.3 - - - +
108A THR* 3.8 3.1 + - + -
112A ASP 3.4 2.1 - - - +
113A VAL* 3.1 4.2 - - - -
114A ILE* 2.8 65.2 + - + +
116A VAL* 4.2 10.3 - - + +
135A LEU* 4.5 11.2 - - + -
138A SER* 5.2 1.6 - - - +
141A GLY 4.6 0.9 - - - +
142A PRO 3.5 12.8 - - - +
143A LEU* 3.8 14.8 - - + -
154A PHE* 3.5 48.0 - - + -
167A VAL* 4.3 16.6 - - + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.8 0.2 - - + -
5A ALA* 4.2 13.0 - - + -
33A VAL* 5.5 0.7 - - + -
44A LEU* 4.0 12.1 - - - +
105A TYR 4.5 0.9 - - - +
106A LEU* 1.3 85.0 - - - +
108A THR* 1.3 68.6 + - - +
111A ALA* 4.5 0.7 - - - -
112A ASP 3.4 7.0 - - - +
113A VAL* 4.5 11.4 - - + -
138A SER* 4.7 0.7 - - - -
141A GLY* 4.3 1.0 - - - -
142A PRO* 3.1 29.8 + - + +
144A LEU* 3.7 30.1 - - + -
29B ILE* 3.9 29.6 - - + -
31B LEU* 3.8 13.5 - - + -
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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