Contacts of the helix formed by residues 6 - 20 (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 TYR 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 4.2 6.5 - - + -
3A ALA* 4.4 4.2 + - - +
4A PHE* 3.0 27.1 + - + -
5A ASN* 1.3 72.0 + - - +
7A ALA* 1.3 57.3 + - - +
9A ALA* 3.4 6.9 + - - +
10A LEU* 3.0 28.9 + - - +
347A VAL* 4.3 8.3 - - - +
350A ILE* 4.6 0.4 - - + -
351A ASN* 2.7 36.4 + - - -
354A LEU* 3.6 24.5 - - + -
437A LEU* 4.1 10.7 - - + +
440A LEU* 3.7 42.2 - - + -
441A VAL* 3.6 20.9 - - + +
444A TYR* 3.9 28.8 - + + -
445A GLY 4.0 11.6 + - - +
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Residues in contact with ALA 7 (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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5A ASN* 3.2 2.3 + - - +
6A TYR* 1.3 75.1 - - - +
8A GLU* 1.3 61.0 + - - +
10A LEU* 3.4 2.3 + - - +
11A GLN* 2.9 28.4 + - - +
87A SER* 3.9 24.5 - - - -
441A VAL* 3.6 13.3 - - + +
445A GLY 4.4 1.4 + - - -
446A GLY* 3.5 33.4 - - - +
447A THR 3.7 9.0 - - - +
448A PRO* 3.9 6.5 - - + +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.1 37.0 + - - +
7A ALA* 1.3 73.4 - - - +
9A ALA* 1.3 61.3 + - - +
11A GLN* 3.2 12.8 + - - +
12A LYS* 2.8 61.1 + - - +
367A PHE* 3.5 21.3 - - + -
368A GLY 5.0 1.4 + - - -
447A THR 4.2 2.2 + - - +
448A PRO* 4.6 2.5 - - - -
449A LEU* 3.9 31.2 - - + +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN 3.2 9.9 + - - +
6A TYR* 3.7 8.5 - - - +
7A ALA 3.3 0.2 - - - -
8A GLU* 1.3 80.5 - - - +
10A LEU* 1.3 56.9 + - - +
12A LYS* 3.3 5.7 + - - +
13A SER* 2.9 27.7 + - - -
354A LEU* 4.2 16.6 - - + -
364A VAL* 5.5 3.7 - - + +
367A PHE* 3.9 20.6 - - + -
400A GLY* 5.1 1.6 - - - -
433A PHE* 5.1 4.3 - - + -
437A LEU* 3.8 23.1 - - + +
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Residues in contact with LEU 10 (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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6A TYR 3.0 17.4 + - - +
7A ALA* 3.8 4.7 - - - +
9A ALA* 1.3 72.7 - - - +
11A GLN* 1.3 66.4 + - - +
13A SER* 3.0 12.9 + - - -
14A MET* 3.0 19.0 + - + +
83A GLY 4.3 2.2 - - - +
84A TYR* 3.8 36.3 - - + +
87A SER* 3.5 24.9 - - - +
89A GLN* 4.4 4.9 - - + -
434A SER* 3.6 34.5 - - - +
437A LEU* 3.7 10.7 - - + +
438A ALA* 4.0 22.7 - - + +
441A VAL* 4.5 2.5 - - + -
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Residues in contact with GLN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 2.9 17.7 + - - +
8A GLU* 3.3 10.9 - - - +
10A LEU* 1.3 79.1 - - - +
12A LYS* 1.3 60.9 + - - +
14A MET* 3.5 5.0 + - - +
15A PHE* 3.5 13.3 + - - +
30A ARG* 4.8 4.7 + - - +
89A GLN* 3.4 33.2 - - - +
92A TYR* 6.4 0.2 - - + -
448A PRO* 3.7 10.4 - - + +
449A LEU* 3.0 51.1 + - - +
452A PHE* 3.7 38.4 + - + +
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Residues in contact with LYS 12 (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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8A GLU* 2.8 50.3 + - + +
9A ALA* 3.7 5.4 - - - +
11A GLN* 1.3 74.8 - - + +
13A SER* 1.3 65.2 + - - +
15A PHE* 3.2 2.6 + - - +
16A PHE 3.1 8.0 + - - -
364A VAL* 5.6 0.2 - - + -
366A GLY 2.7 31.2 + - - +
367A PHE* 4.2 13.7 - - + +
399A TYR* 3.1 33.1 - - + +
400A GLY* 3.5 17.3 - - - +
449A LEU* 4.1 13.1 - - - +
452A PHE* 3.6 35.9 - - + -
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 2.9 14.9 + - - -
10A LEU* 3.0 13.7 + - - -
12A LYS* 1.3 77.3 - - - +
14A MET* 1.3 65.6 + - - +
16A PHE* 3.2 17.4 + - - +
17A TYR* 3.3 12.5 - - - -
400A GLY* 3.9 5.4 - - - -
430A ASN* 2.9 27.9 + - - +
433A PHE* 4.6 2.7 - - - -
434A SER* 2.6 29.4 + - - -
437A LEU* 4.8 5.8 - - - -
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Residues in contact with MET 14 (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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10A LEU* 3.0 22.4 + - + +
11A GLN 3.7 7.6 - - - +
12A LYS 3.2 0.2 - - - -
13A SER* 1.3 79.9 - - - +
15A PHE* 1.3 60.4 + - - +
17A TYR* 3.5 10.8 + - + -
18A GLU* 3.4 13.2 + - - +
30A ARG* 4.1 4.9 + - - +
73A LEU* 4.4 7.4 - - + -
84A TYR* 4.0 23.6 - - + +
89A GLN* 4.1 20.6 - - + +
92A TYR* 4.0 18.8 - - + -
93A LEU* 3.8 23.6 - - + -
96A ASN* 3.2 35.3 + - - +
434A SER* 4.0 21.3 - - - +
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Residues in contact with PHE 15 (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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11A GLN 3.5 1.8 + - - -
12A LYS 3.2 9.1 + - - +
14A MET* 1.3 76.0 - - - +
16A PHE* 1.3 67.9 + - - +
18A GLU* 3.1 5.4 + - - +
19A ALA* 3.0 21.1 + - + +
30A ARG* 3.6 24.1 - - - +
31A VAL* 3.7 38.8 - - + +
33A TRP* 4.5 10.8 - + - -
397A VAL 4.3 4.7 - - - -
398A LEU 5.0 0.2 - - - -
399A TYR* 3.7 43.5 - + + -
452A PHE* 3.8 21.8 - + + -
453A PRO* 3.4 41.7 - - + -
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Residues in contact with PHE 16 (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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12A LYS 3.1 6.7 + - - +
13A SER 3.2 11.2 + - - +
15A PHE* 1.3 76.5 - - - +
17A TYR* 1.3 70.0 + + - +
19A ALA* 3.0 17.7 + - - +
20A GLN* 3.2 41.6 + - + +
398A LEU* 3.9 22.9 - - + -
399A TYR 3.5 16.9 + - - +
400A GLY 4.1 6.1 - - - -
401A ALA* 3.5 30.1 - - + -
425A VAL* 4.7 4.5 - - + -
426A ALA 3.8 37.5 - - - -
427A THR* 4.2 7.2 - - - -
430A ASN* 3.7 27.6 - - + -
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Residues in contact with TYR 17 (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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13A SER 3.3 24.0 + - - -
14A MET* 3.8 9.2 - - + +
15A PHE 3.3 0.4 - - - -
16A PHE* 1.3 84.5 - + - +
18A GLU* 1.3 62.7 + - - +
20A GLN* 3.2 17.1 + - - +
21A ARG* 3.6 5.5 + - - +
53A TRP* 3.8 36.2 + + + -
69A THR* 3.6 23.9 - - + +
73A LEU* 4.0 15.7 - - + -
96A ASN* 3.7 25.8 - - + +
427A THR* 2.7 37.2 + - + -
430A ASN* 3.0 37.4 - - + -
431A ALA* 3.0 6.2 + - - -
434A SER* 4.1 11.9 - - - -
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Residues in contact with GLU 18 (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 3.4 9.0 + - - +
15A PHE* 3.1 11.4 + - - +
17A TYR* 1.3 78.1 - - - +
19A ALA* 1.3 61.5 + - - +
20A GLN 3.2 0.2 - - - -
21A ARG* 3.3 56.8 + - - +
25A LEU* 5.5 1.6 - - - +
28A ASN* 4.3 2.1 - - - +
29A ASN* 3.7 12.1 - - - +
30A ARG* 2.9 66.0 + - - +
31A VAL* 4.1 12.6 - - + +
34A ARG* 4.7 2.8 + - - +
92A TYR* 4.9 3.3 - - - -
95A ASP* 5.2 4.1 - - - +
96A ASN* 3.9 5.3 + - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.0 14.3 + - + +
16A PHE* 3.0 12.7 + - - +
18A GLU* 1.3 76.2 - - - +
20A GLN* 1.3 62.1 + - - +
21A ARG 3.3 0.7 - - - -
31A VAL* 3.9 16.5 - - + +
33A TRP* 4.2 12.8 - - + -
34A ARG* 2.8 28.7 + - - -
54A TYR* 5.4 0.3 - - - -
377A HIS* 4.9 5.0 - - - -
398A LEU* 3.9 24.5 - - + -
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Residues in contact with GLN 20 (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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16A PHE* 3.4 42.0 - - + +
17A TYR* 3.2 11.6 + - - +
18A GLU 3.2 1.2 - - - -
19A ALA* 1.3 78.9 - - - +
21A ARG* 1.3 62.7 + - - +
34A ARG* 4.1 0.4 - - - -
53A TRP* 3.4 11.1 - - + -
54A TYR* 2.8 66.8 + - - +
55A ASP 3.7 8.1 + - - -
56A ALA* 3.0 22.0 + - - +
377A HIS* 2.7 31.0 + - - -
398A LEU* 4.6 0.7 - - - +
427A THR* 4.1 5.9 - - + +
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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