Contacts of the helix formed by residues 6 - 20 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO* 4.2 6.5 - - + -
3B ALA* 4.3 8.1 + - - +
4B PHE* 3.0 22.7 + - + -
5B ASN* 1.3 71.6 + - - +
7B ALA* 1.3 57.5 + - - +
9B ALA* 3.4 7.0 + - - +
10B LEU* 3.0 29.1 + - - +
347B VAL* 4.3 8.3 - - - +
350B ILE* 4.6 0.4 - - + -
351B ASN* 2.7 35.1 + - - -
354B LEU* 3.6 25.1 - - + -
437B LEU* 4.0 12.9 - - + +
440B LEU* 3.7 39.9 - - + -
441B VAL* 3.6 20.5 - - + +
444B TYR* 3.8 28.4 - + + -
445B GLY 4.0 12.2 + - - +
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN* 3.2 9.1 + - - +
6B TYR* 1.3 75.1 - - - +
8B GLU* 1.3 60.4 + - - +
10B LEU* 3.4 3.0 + - - +
11B GLN* 2.9 28.8 + - - +
87B SER* 4.0 23.5 - - - -
441B VAL* 3.6 13.9 - - + +
445B GLY 4.4 1.4 + - - -
446B GLY* 3.5 25.6 - - - +
447B THR 3.8 9.2 - - - +
448B PRO* 3.8 6.5 - - + +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN* 3.1 36.7 + - - +
7B ALA* 1.3 74.4 - - - +
9B ALA* 1.3 60.9 + - - +
11B GLN* 3.2 11.6 + - - +
12B LYS* 2.8 58.7 + - - +
367B PHE* 3.6 21.0 - - + -
368B GLY 5.0 1.6 + - - -
447B THR 4.2 2.4 + - - +
448B PRO* 4.6 2.0 - - - -
449B LEU* 3.7 35.2 - - + +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN 3.2 9.9 + - - +
6B TYR* 3.6 9.4 - - - +
8B GLU* 1.3 79.4 - - - +
10B LEU* 1.3 56.1 + - - +
12B LYS* 3.2 5.8 + - - +
13B SER* 2.9 26.5 + - - -
354B LEU* 4.2 16.2 - - + -
364B VAL* 5.5 4.3 - - + +
367B PHE* 3.9 21.4 - - + -
400B GLY* 5.1 1.7 - - - +
433B PHE* 5.1 4.0 - - + -
437B LEU* 3.8 22.5 - - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR 3.0 17.6 + - - +
7B ALA* 3.7 4.7 - - - +
9B ALA* 1.3 73.6 - - - +
11B GLN* 1.3 66.3 + - - +
13B SER* 3.0 12.2 + - - -
14B MET* 3.0 19.6 + - + +
83B GLY 4.4 2.5 - - - +
84B TYR* 3.9 36.1 - - + +
87B SER* 3.6 24.7 - - - +
89B GLN* 4.4 4.9 - - + -
434B SER* 3.7 34.3 - - - +
437B LEU* 3.7 10.7 - - + +
438B ALA* 4.0 23.6 - - + +
441B VAL* 4.6 2.7 - - + -
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA 2.9 17.3 + - - +
8B GLU* 3.3 7.0 - - - +
10B LEU* 1.3 78.8 - - - +
12B LYS* 1.3 61.7 + - + +
14B MET* 3.5 10.0 + - - +
15B PHE* 3.5 11.4 + - - +
30B ARG* 4.8 5.7 + - - +
89B GLN* 3.5 37.0 - - - +
448B PRO* 3.8 8.4 - - + +
449B LEU* 2.9 56.2 + - - +
452B PHE* 3.6 33.7 + - + +
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.8 47.2 + - + +
9B ALA* 3.8 4.5 - - - +
11B GLN* 1.3 75.7 - - + +
13B SER* 1.3 64.4 + - - +
15B PHE* 3.2 2.4 + - - +
16B PHE 3.1 8.0 + - - -
364B VAL* 5.6 0.2 - - + -
366B GLY 2.7 30.4 + - - +
367B PHE* 4.2 13.9 - - + +
399B TYR* 3.1 34.9 - - + +
400B GLY* 3.5 18.6 - - - +
449B LEU* 3.7 20.4 - - - +
452B PHE* 3.6 31.6 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 2.9 14.3 + - - -
10B LEU* 3.0 14.1 + - - -
12B LYS* 1.3 76.1 - - - +
14B MET* 1.3 66.9 + - - +
16B PHE* 3.2 17.3 + - - +
17B TYR* 3.3 11.4 - - - -
400B GLY* 3.9 6.0 - - - -
430B ASN* 2.9 28.2 + - - +
433B PHE* 4.6 2.5 - - - -
434B SER* 2.6 28.8 + - - -
437B LEU* 4.8 5.8 - - - -
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Residues in contact with MET 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.0 21.8 + - + +
11B GLN 3.7 8.3 - - - +
12B LYS 3.2 0.2 - - - -
13B SER* 1.3 80.1 - - - +
15B PHE* 1.3 59.0 + - - +
17B TYR* 3.5 11.8 + - + -
18B GLU* 3.4 13.3 + - - +
30B ARG* 4.1 4.8 + - - +
73B LEU* 4.4 7.6 - - + -
84B TYR* 4.0 25.6 - - + +
89B GLN* 4.1 20.9 - - + +
92B TYR* 4.1 17.9 - - + -
93B LEU* 3.9 22.4 - - - -
96B ASN* 3.2 33.2 + - - +
434B SER* 4.0 19.1 - - - +
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Residues in contact with PHE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN 3.5 2.6 + - - +
12B LYS 3.2 8.9 + - - +
14B MET* 1.3 75.6 - - - +
16B PHE* 1.3 66.0 + - - +
18B GLU* 3.1 5.6 + - - +
19B ALA* 3.0 20.4 + - + +
30B ARG* 3.6 24.2 - - + +
31B VAL* 3.7 39.0 - - + -
33B TRP* 4.5 11.4 - + - -
397B VAL 4.3 4.7 - - - -
398B LEU 5.0 0.2 - - - -
399B TYR* 3.7 45.8 - + + -
452B PHE* 3.8 21.8 - + + -
453B PRO* 3.5 37.9 - - + -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 3.1 7.7 + - - +
13B SER* 3.2 11.2 - - - +
15B PHE* 1.3 76.5 - - - +
17B TYR* 1.3 69.7 + + - +
19B ALA* 3.0 18.4 + - - +
20B GLN* 3.2 40.1 + - + +
398B LEU* 3.9 23.3 - - + -
399B TYR 3.5 16.3 + - - +
400B GLY 4.1 5.8 - - - -
401B ALA* 3.5 29.6 - - + -
425B VAL* 4.6 4.0 - - + -
426B ALA 3.8 39.7 - - - -
427B THR* 4.1 7.4 - - - -
430B ASN* 3.7 27.6 - - + -
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.3 23.8 + - - -
14B MET* 4.3 9.2 - - + -
15B PHE 3.3 0.6 - - - -
16B PHE* 1.3 83.8 - + - +
18B GLU* 1.3 61.6 + - - +
20B GLN* 3.2 17.2 + - - +
21B ARG* 3.7 5.4 + - - +
53B TRP* 3.8 35.1 + + + -
69B THR* 3.5 21.6 - - + +
73B LEU* 4.0 18.2 - - + -
96B ASN* 3.7 26.0 - - + +
427B THR* 2.7 38.1 + - + -
430B ASN* 3.0 36.1 + - + -
431B ALA* 3.0 6.1 + - - -
434B SER* 4.1 12.3 - - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET 3.4 8.6 + - - +
15B PHE* 3.1 11.8 + - - +
17B TYR* 1.3 78.9 - - - +
19B ALA* 1.3 62.1 + - - +
21B ARG* 3.2 56.6 + - - +
25B LEU* 5.5 1.6 - - - +
28B ASN* 4.3 2.3 - - - +
29B ASN* 3.7 12.1 - - - +
30B ARG* 2.8 66.0 + - - +
31B VAL* 4.1 12.8 - - + +
34B ARG* 4.7 2.9 + - - +
92B TYR* 4.9 3.6 - - - -
95B ASP* 5.3 2.9 - - - +
96B ASN* 3.9 5.9 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.0 15.9 + - + +
16B PHE* 3.0 12.7 + - - +
18B GLU* 1.3 75.0 - - - +
20B GLN* 1.3 62.7 + - - +
21B ARG 3.3 0.4 - - - -
31B VAL* 3.9 17.0 - - + +
33B TRP* 4.2 13.5 - - + -
34B ARG* 2.8 29.1 + - - -
54B TYR* 5.5 0.2 - - - -
377B HIS* 4.9 5.0 - - - -
398B LEU* 3.9 23.8 - - + -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.4 42.2 - - + +
17B TYR* 3.2 12.3 + - - +
18B GLU 3.1 0.8 - - - -
19B ALA* 1.3 79.3 - - - +
21B ARG* 1.3 61.6 + - - +
34B ARG* 4.1 0.9 - - - -
53B TRP* 3.4 10.2 - - + -
54B TYR* 2.8 66.5 + - - +
55B ASP 3.7 8.3 + - - -
56B ALA* 3.0 22.0 + - - +
377B HIS* 2.7 30.8 + - - -
398B LEU* 4.6 0.9 - - - +
427B THR* 4.1 7.3 - - + +
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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
------------------------------------------------------------
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