Contacts of the strand formed by residues 114 - 120 (chain A) in PDB entry 1T6M
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 ILE 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A MET* 4.2 9.6 - - + -
68A ARG* 3.6 7.9 - - - -
70A PHE* 3.9 26.9 - - + -
98A PHE* 3.9 27.8 - - + -
102A ALA* 4.2 7.6 - - + +
105A PHE* 4.0 23.8 - - + -
106A LEU* 3.9 20.6 - - + +
113A THR* 1.3 83.5 + - - +
115A ILE* 1.3 60.5 + - - +
161A LYS 3.1 4.8 + - - -
162A ILE* 3.1 27.1 - - + +
163A VAL 2.7 31.7 + - - -
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Residues in contact with ILE 115 (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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18A MET* 5.6 0.2 - - + -
27A LEU* 4.0 18.2 - - + -
32A ILE* 4.0 13.2 - - + -
68A ARG* 2.7 16.6 + - + +
69A ILE* 3.2 29.3 - - + -
70A PHE* 2.9 28.6 + - - -
113A THR* 4.6 7.2 - - + -
114A ILE* 1.3 74.9 - - - +
116A MET* 1.3 62.0 + - - +
117A SER 4.2 0.2 - - - -
163A VAL* 3.2 28.0 - - + +
165A LEU* 4.6 15.0 - - + -
177A TYR* 5.1 1.6 - - + -
274A TRP* 3.8 39.5 - - + -
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Residues in contact with MET 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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70A PHE 3.6 2.9 - - - -
72A ILE* 3.1 27.4 - - + -
95A LEU* 4.0 20.0 - - + -
98A PHE* 3.6 18.6 - - + -
99A ILE* 3.5 27.4 - - - -
114A ILE 4.0 0.2 + - - -
115A ILE* 1.3 72.6 - - - +
117A SER* 1.3 61.2 + - - +
118A LEU* 4.0 26.0 - - + -
136A PHE* 4.0 16.8 - - + -
146A PHE* 4.2 7.6 - - + -
162A ILE* 3.8 15.5 - - + -
163A VAL 2.8 9.5 + - - -
164A LEU* 3.4 21.1 - - + +
165A LEU* 2.8 24.8 + - - -
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Residues in contact with SER 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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69A ILE* 5.4 3.2 - - - +
70A PHE 2.9 9.6 + - - +
71A ASP* 3.4 28.9 + - - -
72A ILE* 3.0 26.4 + - - +
115A ILE* 4.2 1.2 - - - +
116A MET* 1.3 73.0 - - - +
118A LEU* 1.3 61.2 + - - +
119A LYS* 5.8 0.9 - - - +
165A LEU* 3.1 34.2 - - - +
167A ARG* 4.2 11.5 - - - +
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Residues in contact with LEU 118 (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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72A ILE* 3.9 27.6 - - + +
74A GLY 4.5 4.0 - - - +
82A ILE* 4.9 2.7 - - + -
95A LEU* 4.6 11.0 - - + -
116A MET* 3.8 9.0 + - + -
117A SER* 1.3 74.2 - - - +
119A LYS* 1.3 66.8 + - - +
132A PHE* 4.0 31.0 - - + -
136A PHE* 3.4 48.9 - - + -
164A LEU* 3.9 14.6 - - + -
165A LEU 3.1 9.3 + - - -
167A ARG* 2.8 32.1 + - - +
168A TYR* 3.5 9.7 + - + -
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Residues in contact with LYS 119 (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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71A ASP* 5.7 0.4 - - - +
72A ILE 3.1 6.2 + - - +
73A ASP* 3.5 19.3 + - - +
74A GLY 3.0 26.2 + - - -
117A SER* 5.8 0.9 - - - +
118A LEU* 1.3 75.3 - - - +
120A LYS* 1.3 72.2 + - - +
121A GLU* 3.1 27.5 + - - +
132A PHE* 3.6 9.3 - - - -
167A ARG* 3.7 25.1 - - + +
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Residues in contact with LYS 120 (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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74A GLY 3.8 4.0 - - - +
119A LYS* 1.3 84.8 - - - +
121A GLU* 1.3 60.6 + - - +
122A TYR 3.4 19.7 + - - +
123A GLU* 3.1 31.0 + - - +
124A ASP* 3.3 18.4 + - - +
132A PHE* 3.5 44.6 - - + +
167A ARG 4.3 3.8 + - - -
168A TYR* 4.8 6.2 - - + +
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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