Contacts of the helix formed by residues 106 - 117 (chain A) in PDB entry 3FTC
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 VAL 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASP* 5.8 2.0 - - - +
85A SER* 5.1 10.3 - - - +
103A PRO* 3.7 25.6 - - + +
105A ASN* 1.3 94.6 - - - +
107A ALA* 1.3 66.8 + - - +
108A SER 3.3 2.9 - - - -
109A LEU* 3.1 13.9 + - + -
110A ILE* 2.8 46.0 + - + +
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Residues in contact with ALA 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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102A LEU* 3.8 26.0 - - + +
103A PRO 2.9 18.1 + - - +
104A TYR* 4.0 9.8 + - - +
105A ASN 3.8 1.0 - - - -
106A VAL* 1.3 76.4 - - - +
108A SER* 1.3 64.9 + - - +
110A ILE* 3.4 2.0 + - - +
111A ILE* 3.0 30.9 + - - +
128A VAL* 4.2 17.5 - - + -
129A GLN 5.8 0.9 - - - +
132A VAL* 5.0 10.3 - - + -
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Residues in contact with SER 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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104A TYR 5.1 1.9 + - - -
105A ASN 5.5 0.2 - - - -
106A VAL 3.3 0.8 - - - -
107A ALA* 1.3 77.2 - - - +
109A LEU* 1.3 64.7 + - - +
111A ILE* 3.4 3.2 + - - -
112A GLU* 3.0 27.5 + - - +
132A VAL* 4.7 17.5 - - - +
145A LEU* 3.4 28.3 - - - +
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Residues in contact with LEU 109 (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 SER* 3.8 23.8 - - - +
86A LYS* 6.5 0.4 - - - -
105A ASN 4.0 20.2 - - - +
106A VAL* 3.1 10.6 + - + +
108A SER* 1.3 81.6 - - - +
110A ILE* 1.3 61.2 + - - +
112A GLU* 3.5 22.1 + - - +
113A ASN* 3.0 28.2 + - - +
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Residues in contact with ILE 110 (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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37A VAL* 4.0 32.5 - - + +
84A ALA* 4.2 17.9 - - + +
85A SER* 4.0 25.4 - - - +
89A PHE* 4.8 0.6 - - + -
102A LEU* 3.9 26.7 - - + -
103A PRO* 4.8 3.4 - - + -
106A VAL* 2.8 40.7 + - + +
107A ALA 3.8 3.6 - - - +
109A LEU* 1.3 73.9 - - - +
111A ILE* 1.3 59.7 + - - +
113A ASN* 3.2 3.5 + - - +
114A THR* 2.9 37.6 + - - +
126A PHE* 4.5 1.8 - - + -
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Residues in contact with ILE 111 (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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102A LEU* 3.8 11.4 - - + -
107A ALA 3.0 23.4 + - - +
108A SER* 3.9 4.7 - - - +
110A ILE* 1.3 71.1 - - - +
112A GLU* 1.3 67.0 + - - +
114A THR* 3.2 9.3 + - - -
115A VAL* 3.1 21.2 + - - +
126A PHE* 3.9 15.9 - - + -
128A VAL* 4.0 24.0 - - + -
132A VAL* 4.6 4.5 - - + -
136A LEU* 3.6 30.3 - - + -
145A LEU* 4.5 4.5 - - + -
149A VAL* 3.7 26.7 - - + -
177A ILE* 4.6 1.6 - - + -
179A LEU* 4.4 15.7 - - + -
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Residues in contact with GLU 112 (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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108A SER 3.0 17.7 + - - +
109A LEU* 3.6 25.9 - - - +
111A ILE* 1.3 76.5 - - - +
113A ASN* 1.3 62.4 + - - +
115A VAL* 3.1 6.3 + - - +
116A TYR* 2.8 49.8 + - + -
144A TRP* 3.4 28.2 - - + -
145A LEU* 3.8 17.2 - - + +
148A PHE* 3.9 7.9 - - + -
194A LYS* 2.6 29.0 + - - +
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Residues in contact with ASN 113 (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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84A ALA 2.9 22.7 + - - +
85A SER 3.5 16.9 - - - +
86A LYS* 3.7 6.3 - - - +
87A PHE 2.7 34.6 + - - +
88A PRO* 5.3 0.2 - - - +
89A PHE* 3.9 6.4 - - - -
109A LEU 3.0 17.6 + - - +
110A ILE 3.2 5.6 + - - +
112A GLU* 1.3 72.9 - - - +
114A THR* 1.3 66.0 + - - +
116A TYR* 3.3 17.1 + - - +
117A ASN* 2.9 33.5 + - - -
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Residues in contact with THR 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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89A PHE* 3.4 23.1 - - + -
98A VAL* 4.2 3.7 - - + +
110A ILE* 2.9 15.1 + - - +
111A ILE* 3.2 9.6 + - - -
113A ASN* 1.3 75.7 - - - +
115A VAL* 1.3 58.8 + - - +
117A ASN* 2.9 28.6 + - - +
118A LYS* 3.2 2.3 + - - -
121A VAL* 3.9 29.6 - - + +
124A ALA* 4.3 16.2 - - + -
126A PHE* 3.5 20.2 - - + -
153A TYR* 4.3 4.8 + - + +
179A LEU* 5.1 7.2 - - + -
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Residues in contact with VAL 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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111A ILE* 3.1 16.4 + - + +
112A GLU 3.1 7.6 + - - +
114A THR* 1.3 73.2 - - - +
116A TYR* 1.3 66.3 + - - +
117A ASN 3.0 1.6 - - - -
118A LYS* 2.8 30.4 + - - +
148A PHE* 3.4 29.2 - - + +
149A VAL* 3.7 31.4 - - + -
152A PHE* 3.5 33.9 - - + -
153A TYR* 4.3 13.2 - - + -
179A LEU* 5.2 1.8 - - + -
190A LEU* 4.2 1.8 - - + +
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Residues in contact with TYR 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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112A GLU* 2.8 57.4 + - + -
113A ASN* 3.3 22.0 + - - +
115A VAL* 1.3 75.6 - - - +
117A ASN* 1.3 61.9 + - - +
118A LYS* 3.5 2.1 + - - +
119A ASP* 5.0 2.6 + - - +
148A PHE* 3.9 15.0 - + - -
190A LEU* 3.4 49.6 - - + +
191A LYS* 4.4 18.3 - - + +
194A LYS* 3.0 21.0 + - + +
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Residues in contact with ASN 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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87A PHE 3.8 10.1 + - - -
88A PRO* 3.5 9.4 - - - +
89A PHE* 3.1 36.5 + - + +
90A CYS* 3.0 37.5 + - - +
113A ASN* 2.9 27.0 + - - +
114A THR 2.9 12.7 + - - +
116A TYR* 1.3 79.6 - - - +
118A LYS* 1.3 63.1 + - - +
119A ASP* 3.2 3.4 - - - -
120A CYS* 3.1 12.8 + - - -
121A VAL* 3.4 9.5 + - + +
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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