Contacts of the helix formed by residues 2 - 14 (chain l) in PDB entry 5XTD
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 THR 2 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83b HIS* 3.4 33.4 - - + +
86b MET* 4.3 13.7 - - + -
97b ILE* 6.2 2.0 - - + -
99b GLU* 5.6 1.3 - - - -
31d PHE* 5.5 0.2 - - - -
1l MET* 1.3 81.9 - - - +
3l MET* 1.3 64.0 + - - +
4l HIS 3.0 0.4 - - - -
5l THR* 2.4 38.1 + - + +
6l THR* 2.9 9.9 + - + -
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Residues in contact with MET 3 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27d MET* 4.6 6.5 - - + +
28d MET* 3.3 48.0 - - + +
31d PHE* 3.4 43.4 - - + -
1l MET* 2.9 8.1 - - + +
2l THR* 1.3 80.4 - - - +
4l HIS* 1.3 66.4 + - + +
6l THR* 3.4 8.5 - - - -
7l MET* 2.9 50.6 + - + +
49l PHE* 5.6 7.2 - - + -
50l PRO* 6.2 0.2 - - + -
53l MET* 3.5 35.7 - - + -
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Residues in contact with HIS 4 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1l MET 3.0 25.3 + - - +
3l MET* 1.3 85.6 - - + +
5l THR* 1.3 61.2 + - - +
7l MET* 4.0 2.9 - - - +
8l ALA* 3.0 25.0 + - + +
50l PRO* 4.1 17.4 + - + +
53l MET* 3.9 22.6 - - + +
54l PHE* 4.7 2.7 - - - -
57l LEU* 5.9 2.6 - - + +
59l GLN* 4.1 25.0 + - + +
60l GLU* 5.4 0.2 - - - -
61l VAL* 3.6 30.1 - - + +
82l LEU* 5.1 6.3 + - + +
87l MET* 2.7 39.7 - - + +
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Residues in contact with THR 5 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86b MET* 4.4 9.1 - - - +
97b ILE* 4.6 15.9 - - + +
99b GLU* 4.5 7.4 - - - +
1l MET 4.3 7.6 - - - +
2l THR* 2.4 31.6 + - + +
4l HIS* 1.3 77.0 - - - +
6l THR* 1.3 66.2 + - - +
8l ALA* 2.9 8.2 + - - +
9l THR* 2.8 32.9 + - - +
61l VAL* 4.0 32.1 - - + -
63l ILE* 4.7 13.0 - - + -
82l LEU* 5.3 2.2 - - - -
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Residues in contact with THR 6 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79b VAL* 5.4 5.6 - - - -
82b ILE* 4.2 9.4 - - + +
83b HIS* 3.3 41.7 - - + -
86b MET* 3.8 12.8 - - + -
31d PHE* 3.5 13.4 - - - -
2l THR* 2.9 13.8 + - + +
3l MET* 3.2 14.6 + - - -
5l THR* 1.3 86.6 + - - +
7l MET* 1.3 62.3 + - - +
9l THR* 3.0 9.1 + - - -
10l LEU* 2.9 30.4 + - - +
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Residues in contact with MET 7 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79b VAL* 5.6 4.9 - - - -
31d PHE* 4.3 20.4 - - - -
3l MET* 2.9 45.9 + - + +
4l HIS* 4.0 1.6 - - - +
6l THR* 1.3 76.3 + - - +
8l ALA* 1.3 68.1 + - - +
10l LEU* 3.0 24.9 + - + +
11l THR* 3.0 19.3 + - - +
46l ILE* 4.0 30.1 - - + +
49l PHE* 4.0 27.1 - - + -
50l PRO* 3.6 20.2 - - + -
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Residues in contact with ALA 8 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4l HIS* 3.0 17.4 + - + +
5l THR 2.9 9.3 + - - +
7l MET* 1.3 75.8 - - - +
9l THR* 1.3 60.3 + - - +
11l THR* 2.5 31.4 + - - -
12l LEU* 3.8 5.6 + - - +
50l PRO* 4.3 10.2 - - + +
82l LEU* 3.8 34.1 - - + -
87l MET* 6.0 2.7 - - - -
90l ILE* 5.6 1.2 - - - +
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Residues in contact with THR 9 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82b ILE* 3.2 23.0 - - - +
86b MET* 3.8 21.1 - - + -
5l THR 2.8 15.4 + - - +
6l THR 3.0 10.2 + - - -
8l ALA* 1.3 72.7 - - + +
10l LEU* 1.3 68.5 + - - +
12l LEU* 3.1 14.3 + - + +
13l THR* 2.9 32.1 + - - +
63l ILE* 3.8 20.2 - - + -
80l PHE* 6.5 0.7 - - + -
82l LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 10 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74b HIS 5.7 2.7 - - - +
75b VAL* 4.4 10.5 - - + +
78b PRO* 4.8 7.0 - - + -
79b VAL* 3.4 45.8 - - + +
82b ILE* 4.8 4.7 - - + -
6l THR 2.9 21.0 + - - +
7l MET* 3.0 18.3 + - + +
9l THR* 1.3 78.4 + - - +
11l THR* 1.3 63.5 + - - +
13l THR* 3.4 9.9 - - - +
14l SER* 2.9 37.7 + - - +
46l ILE* 3.5 32.5 - - + -
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Residues in contact with THR 11 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7l MET 3.0 17.2 + - - +
8l ALA* 2.5 20.5 + - - +
10l LEU* 1.3 79.6 - - - +
12l LEU* 1.3 66.1 + - - +
14l SER* 2.8 16.9 + - - -
15l LEU* 4.1 10.6 - - - +
43l THR* 4.5 8.9 - - - -
46l ILE* 4.6 7.6 - - + +
47l SER* 3.7 37.9 - - - +
50l PRO* 4.8 4.7 - - + -
90l ILE* 4.4 19.7 - - + +
94l LEU* 5.5 3.6 - - - +
129l LEU* 5.4 1.5 - - - +
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Residues in contact with LEU 12 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8l ALA 4.2 6.3 - - - +
9l THR* 3.1 12.5 + - + +
10l LEU 3.1 0.2 - - - -
11l THR* 1.3 87.4 + - - +
13l THR* 1.3 68.7 + - + +
14l SER 3.0 2.0 - - - -
15l LEU* 3.0 24.2 + - + +
16l ILE* 4.1 5.1 + - - +
80l PHE* 4.5 24.2 - - + -
82l LEU* 6.3 1.6 - - + -
90l ILE* 4.5 9.9 - - + -
126l ILE* 6.0 3.9 - - + +
129l LEU* 3.6 42.8 - - + -
130l ILE* 6.1 3.4 - - + -
133l THR* 4.5 14.8 - - + +
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Residues in contact with THR 13 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78b PRO* 4.9 4.2 - - - +
82b ILE* 3.4 28.2 - - + +
9l THR* 2.9 25.0 + - - +
10l LEU* 3.3 12.6 + - - +
12l LEU* 1.3 77.3 - - + +
14l SER* 1.3 64.3 + - - +
15l LEU 3.3 0.7 + - - -
16l ILE* 3.3 29.8 + - + +
17l PRO* 3.5 5.0 - - - +
502r PLX 4.6 29.6 - - + +
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Residues in contact with SER 14 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74b HIS* 4.8 12.7 - - - -
78b PRO* 6.1 4.3 - - - -
10l LEU* 2.9 27.2 + - - +
11l THR* 2.8 26.7 + - - -
13l THR* 1.3 80.8 + - - +
15l LEU* 1.3 55.0 + - - +
16l ILE 3.3 0.2 - - - -
17l PRO* 3.1 18.5 - - - +
39l ILE* 3.8 16.0 - - - +
43l THR* 3.1 22.6 - - - +
46l ILE* 6.2 0.7 - - - -
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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