Contacts of the helix formed by residues 90 - 106 (chain A) in PDB entry 1TF4
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 MET 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ALA* 4.6 8.7 - - + +
81A PRO* 3.9 39.0 - - + +
84A TYR* 3.0 26.7 + - + +
85A ILE* 4.3 17.3 - - + +
89A GLN* 1.3 75.9 - - - +
91A PRO* 1.3 69.3 - - + +
93A LEU* 3.2 21.2 + - - -
94A LYS* 3.0 56.0 + - + +
166A VAL* 5.1 2.5 - - + -
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Residues in contact with PRO 91 (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 GLY* 3.7 16.8 - - - +
89A GLN 3.4 1.1 - - - -
90A MET* 1.3 95.8 - - + +
92A TYR* 1.3 73.3 + - + +
94A LYS* 3.5 9.4 + - + +
95A ASP* 3.0 27.5 + - - +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 6.4 0.2 - - + -
14A MET* 4.0 19.3 - - + -
18A GLU* 4.9 3.1 - - - -
30A ARG* 3.7 49.2 + - - +
88A GLY 4.1 16.4 - - - -
89A GLN* 3.0 28.1 + - - +
91A PRO* 1.3 85.7 - - + +
93A LEU* 1.3 66.4 + - - +
95A ASP* 3.3 11.3 + - + +
96A ASN* 2.9 32.1 + - - +
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Residues in contact with LEU 93 (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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14A MET* 3.8 13.6 - - - -
73A LEU* 4.1 28.0 - - + +
77A ALA* 3.3 28.9 - - + -
84A TYR* 3.5 39.0 - - + +
89A GLN 3.0 11.8 + - - +
90A MET* 3.5 23.8 - - - +
92A TYR* 1.3 78.0 - - - +
94A LYS* 1.3 56.9 + - - +
96A ASN* 3.2 5.3 + - + +
97A LEU* 2.9 43.0 + - + +
166A VAL* 4.3 6.7 - - + -
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Residues in contact with LYS 94 (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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90A MET* 3.0 51.3 + - + +
91A PRO* 3.8 7.6 - - + +
93A LEU* 1.3 78.9 - - + +
95A ASP* 1.3 56.5 + - - +
97A LEU* 4.5 1.6 - - - -
98A ARG* 2.9 33.0 + - - +
166A VAL* 3.9 29.8 + - + -
167A PHE* 3.3 25.8 - - + -
170A ASP* 2.6 34.5 + - - +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.2 4.5 - - - +
21A ARG* 3.0 27.2 + - - +
28A ASN* 5.2 9.5 + - - +
91A PRO 3.0 18.8 + - - +
92A TYR* 3.6 14.7 - - + +
93A LEU 3.3 0.4 - - - -
94A LYS* 1.3 75.7 - - - +
96A ASN* 1.3 57.9 + - - +
98A ARG* 3.5 9.7 + - - +
99A TRP* 3.0 28.9 + - - +
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Residues in contact with ASN 96 (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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14A MET* 3.2 41.9 + - - +
17A TYR* 3.7 22.4 - - + +
18A GLU* 3.9 11.6 + - - +
21A ARG* 3.7 16.9 + - - +
53A TRP* 3.5 23.2 + - + -
73A LEU* 5.4 5.4 - - + -
92A TYR* 2.9 21.7 + - - +
93A LEU* 3.5 5.8 - - + +
95A ASP* 1.3 73.3 - - - +
97A LEU* 1.3 64.8 + - + +
99A TRP* 3.2 5.9 + - - +
100A VAL 3.2 17.7 + - - -
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Residues in contact with LEU 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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70A ALA* 3.9 28.0 - - - +
73A LEU* 4.2 17.7 - - + -
74A ALA* 4.1 26.7 - - + +
93A LEU* 2.9 39.2 + - + +
94A LYS 3.9 3.4 - - - +
96A ASN* 1.3 74.2 - - + +
98A ARG* 1.3 60.8 + - - +
100A VAL* 3.2 10.0 - - + +
101A ASN* 2.7 39.2 + - - +
163A SER* 4.1 13.5 - - - +
166A VAL* 4.3 16.8 - - + -
167A PHE* 4.0 11.4 - - + -
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Residues in contact with ARG 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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94A LYS 2.9 18.0 + - - +
95A ASP* 3.8 10.5 - - - +
97A LEU* 1.3 77.3 - - - +
99A TRP* 1.3 63.0 + - - +
102A ASP* 2.9 44.2 + - - +
167A PHE* 3.7 31.5 - - + -
170A ASP* 5.7 1.4 - - - +
171A ASP* 3.2 31.9 + - - +
174A TYR* 3.6 37.7 - - + +
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Residues in contact with TRP 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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21A ARG* 3.7 40.2 - - + +
22A SER 3.1 21.5 - - - -
23A GLY 5.0 0.4 - - - -
24A LYS 3.4 24.0 - - - -
25A LEU* 4.2 4.9 - - + -
26A PRO* 3.7 30.5 - - + -
51A GLY* 4.4 5.6 - - - -
52A GLY 3.0 37.1 + - - +
53A TRP* 3.9 15.9 - + - +
95A ASP* 3.0 15.9 + - - +
96A ASN* 3.4 10.1 - - - +
97A LEU 3.2 0.2 - - - -
98A ARG* 1.3 79.1 - - - +
100A VAL* 1.3 62.6 + - - +
102A ASP* 3.5 7.9 + - - +
103A TYR* 3.5 16.3 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 4.9 0.9 - - - -
53A TRP* 3.8 33.2 - - + -
66A MET* 3.8 27.8 - - + +
70A ALA* 4.0 13.2 - - + -
96A ASN 3.2 8.4 + - - +
97A LEU* 3.2 15.0 - - + +
99A TRP* 1.3 83.1 - - - +
101A ASN* 1.3 72.2 + - - +
103A TYR* 3.2 8.3 + - - +
104A PHE* 3.1 44.3 + - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 5.2 1.2 - - - +
97A LEU* 2.7 31.2 + - - +
100A VAL* 1.3 78.8 - - - +
102A ASP* 1.3 65.6 + - - +
103A TYR 3.0 1.3 - - - -
104A PHE* 3.1 13.5 + - - +
105A ILE* 3.0 28.9 + - - +
159A ALA 4.0 1.2 - - - +
160A MET* 3.7 34.8 - - - +
163A SER* 3.1 29.0 + - - -
167A PHE* 4.9 1.6 - - - -
174A TYR* 3.3 20.6 - - - +
178A LEU* 4.0 13.7 - - + +
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Residues in contact with ASP 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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98A ARG* 2.9 35.7 + - - +
99A TRP* 3.7 8.1 - - - +
100A VAL 3.3 0.2 - - - -
101A ASN* 1.3 76.2 - - - +
103A TYR* 1.3 60.3 + - - +
105A ILE* 3.6 11.8 + - - +
106A LYS* 3.3 30.6 + - - +
174A TYR* 3.0 29.1 + - - -
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Residues in contact with TYR 103 (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 LEU* 3.4 30.0 - - + +
50A THR 3.8 9.4 - - - -
51A GLY* 3.8 14.4 - - - -
52A GLY* 3.6 19.1 - - - +
61A LYS* 3.6 21.3 + - - +
63A GLY* 5.9 3.1 - - - -
66A MET* 3.8 33.7 - - + -
99A TRP 3.5 4.2 + - - +
100A VAL 3.2 8.4 + - - +
101A ASN 3.0 0.8 - - - -
102A ASP* 1.3 76.1 - - - +
104A PHE* 1.3 74.9 + + - +
105A ILE 3.1 1.8 - - - -
106A LYS* 3.1 11.0 + - + +
107A ALA* 2.8 39.7 + - + +
115A TYR* 4.8 9.2 + - - +
116A VAL 5.5 0.9 - - - -
117A GLN 5.1 2.3 + - - -
118A VAL* 3.5 23.2 + - - +
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Residues in contact with PHE 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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63A GLY* 4.9 5.4 - - - -
66A MET* 4.1 19.3 - - + -
67A ALA* 3.6 31.9 - - + -
70A ALA* 4.2 5.4 - - + -
100A VAL* 3.1 34.1 + - + -
101A ASN* 3.1 23.2 + - - +
103A TYR* 1.3 86.2 - + - +
105A ILE* 1.3 62.6 + - - +
107A ALA* 3.4 7.9 + - + +
108A HIS* 3.2 24.8 + - - +
114A LEU* 4.7 3.9 - - + +
156A THR* 3.9 22.8 - - + +
159A ALA* 4.0 19.7 - - + -
160A MET* 3.9 22.0 - - + +
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Residues in contact with ILE 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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101A ASN 3.0 15.1 + - - +
102A ASP* 3.6 13.0 - - - +
104A PHE* 1.3 76.7 - - - +
106A LYS* 1.3 63.6 + - + +
108A HIS 3.0 21.7 + - - +
109A PRO* 5.1 0.3 - - - +
160A MET* 3.7 15.3 - - + -
174A TYR* 4.1 18.2 - - + -
177A THR* 4.4 15.3 - - + -
178A LEU* 4.1 17.0 - - + -
181A HIS* 3.8 27.1 - - + +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.9 3.8 - - - +
48A ASP* 3.4 38.3 + - + +
49A LEU* 3.9 12.5 - - + +
50A THR* 2.8 48.1 + - - +
51A GLY* 4.8 1.6 - - - -
102A ASP* 3.3 18.3 + - - +
103A TYR* 3.1 11.3 + - + +
105A ILE* 1.3 79.8 - - + +
107A ALA* 1.3 59.2 + - - +
108A HIS 3.2 4.3 + - - -
109A PRO* 4.0 12.5 - - - +
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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
------------------------------------------------------------
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