Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 1TFG
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 PRO 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.8 15.9 - - + -
90A TYR 3.8 1.6 - - - +
91A TYR* 3.6 30.0 - - + +
94A LYS 3.7 7.6 - - - +
95A THR* 1.3 91.1 - - + +
97A LYS* 1.3 63.5 + - - +
98A ILE* 4.1 2.3 + - + +
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Residues in contact with LYS 97 (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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88A ILE 3.5 1.7 - - - +
89A LEU* 3.2 7.2 - - - +
90A TYR* 2.8 67.2 + - + +
92A ILE* 3.6 29.8 - - + -
95A THR* 3.8 15.7 - - + +
96A PRO* 1.3 78.6 - - - +
98A ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 98 (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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87A THR* 3.9 21.5 - - + -
88A ILE 3.2 13.7 - - - +
89A LEU* 3.7 30.1 - - + -
96A PRO* 4.1 2.1 + - + -
97A LYS* 1.3 75.9 - - - +
99A GLU* 1.3 67.4 + - - +
100A GLN* 5.1 1.1 - - + +
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Residues in contact with GLU 99 (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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87A THR* 3.3 4.6 - - - -
88A ILE* 2.9 39.9 + - + +
90A TYR* 2.9 42.2 + - + +
97A LYS* 6.0 0.2 - - + -
98A ILE* 1.3 77.3 - - - +
100A GLN* 1.3 66.2 + - - +
101A LEU* 3.4 27.0 + - + +
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Residues in contact with GLN 100 (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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85A PRO* 3.8 34.8 - - + +
86A LEU 3.7 4.0 - - - +
87A THR* 3.7 21.5 + - + +
98A ILE* 5.1 1.6 - - + +
99A GLU* 1.3 75.8 - - - +
101A LEU* 1.3 62.2 + - - +
102A SER* 3.7 5.1 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 6.5 0.4 - - + -
32A TRP* 6.4 0.2 - - + -
33A ILE* 6.2 0.4 - - + -
85A PRO* 3.1 4.4 - - - +
86A LEU 2.9 39.8 + - - +
88A ILE* 3.8 31.2 - - + -
99A GLU* 3.4 35.4 - - + +
100A GLN* 1.3 72.4 - - - +
102A SER* 1.3 61.7 + - - +
104A MET* 3.6 40.0 - - + +
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Residues in contact with SER 102 (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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85A PRO* 4.0 9.2 - - - -
100A GLN* 3.7 7.1 + - - +
101A LEU* 1.3 76.2 - - - +
103A ASN* 1.3 85.3 + - - +
104A MET* 3.3 5.2 + - - +
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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