Contacts of the helix formed by residues 2 - 12 (chain F) in PDB entry 5X11
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 ARG 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0F PRO* 4.2 16.4 - - + +
1F MET* 1.3 73.4 - - - +
3F VAL* 1.3 63.0 + - - +
4F LEU* 3.4 2.9 - - - -
5F LYS* 3.4 17.0 + - + +
6F TYR* 3.3 19.9 - - + -
44F GLU* 3.4 27.9 + - - +
47F LYS* 3.7 22.4 - - - +
48F LEU* 3.9 13.1 - - - +
51F GLU* 2.8 43.0 + - - -
53F PHE* 5.3 3.3 - - - -
14M T 4.4 4.5 - - - +
15M A 2.7 40.2 + - - +
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Residues in contact with VAL 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 3.5 32.8 - - + +
100E LEU* 3.9 18.6 - - + -
1F MET* 3.9 20.4 - - + +
2F ARG* 1.3 70.3 - - - +
4F LEU* 1.3 65.7 - - - +
6F TYR* 3.0 10.7 + - - +
7F ALA* 2.9 18.7 + - - +
34F TRP* 3.5 46.2 - - + -
83F TRP* 4.8 1.6 - - + -
15M A 4.3 2.4 + - - +
16M G 5.7 1.0 + - - +
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Residues in contact with LEU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ARG 3.4 0.6 - - - -
3F VAL* 1.3 77.2 - - - +
5F LYS* 1.3 63.3 + - - +
7F ALA* 3.1 5.2 + - + -
8F ILE* 3.0 40.9 + - + +
26F PHE* 4.4 12.3 - - + -
34F TRP* 4.7 9.3 - - - +
36F ALA* 3.8 22.9 - - + -
40F GLN* 3.5 56.1 - - + +
41F ILE* 4.6 2.0 - - + +
44F GLU* 4.1 18.2 - - + +
16M G 4.4 11.7 + - - +
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Residues in contact with LYS 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ARG* 3.4 32.4 + - + +
3F VAL 3.2 0.4 - - - -
4F LEU* 1.3 79.8 - - - +
6F TYR* 1.3 69.4 + - + +
8F ILE* 3.4 3.3 + - - +
9F LEU* 3.1 29.2 + - + +
44F GLU* 3.3 23.3 + - - +
48F LEU* 4.0 17.3 - - + +
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Residues in contact with TYR 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 4.1 2.8 - - - -
1F MET 3.7 14.1 - - - -
2F ARG* 3.3 29.6 - - + -
3F VAL* 3.0 7.8 + - - +
5F LYS* 1.3 77.9 - - + +
7F ALA* 1.3 67.5 + - - +
9F LEU* 3.4 14.1 + - + +
10F GLY* 2.9 22.3 + - - -
79F GLU* 3.6 47.4 + - + -
80F LEU* 4.2 6.0 - - - +
83F TRP* 3.5 67.7 - + + +
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Residues in contact with ALA 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 3.9 30.3 - - + +
104E PHE* 3.4 8.7 - - - -
3F VAL 2.9 12.0 + - - +
4F LEU* 3.1 13.4 + - - +
6F TYR* 1.3 75.6 - - - +
8F ILE* 1.3 62.0 + - - +
10F GLY 3.3 0.3 + - - -
11F LEU* 3.1 24.2 + - - +
26F PHE* 3.8 24.9 - - + -
34F TRP* 4.5 6.3 - - + -
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Residues in contact with ILE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.0 33.7 + - + +
5F LYS 3.7 6.3 - - - +
7F ALA* 1.3 72.6 - - + +
9F LEU* 1.3 64.8 + - + +
11F LEU* 3.0 19.2 + - - +
12F LEU* 3.2 25.9 + - + +
22F ILE* 3.8 33.0 - - + -
26F PHE* 5.0 0.9 - - + -
41F ILE* 3.9 26.9 - - + +
44F GLU* 4.1 19.3 - - + -
45F LEU* 4.3 11.4 - - + -
48F LEU* 4.3 13.7 - - + -
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LYS* 3.1 22.1 + - + +
6F TYR* 3.9 23.8 - - + +
8F ILE* 1.3 75.2 - - - +
10F GLY* 1.3 61.9 + - - +
12F LEU* 3.4 12.6 + - + -
13F ARG 3.7 7.1 + - - -
48F LEU* 4.6 18.6 - - + -
53F PHE* 4.1 28.5 - - + +
54F ILE* 5.1 5.2 - - + -
72F LEU* 3.6 38.6 - - + +
76F GLY* 4.5 3.8 - - - +
79F GLU* 4.4 22.9 - - + -
80F LEU* 3.8 15.1 - - + +
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Residues in contact with GLY 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 3.3 34.2 - - - -
6F TYR 2.9 11.1 + - - -
9F LEU* 1.3 78.5 - - - +
11F LEU* 1.3 59.1 + - - +
13F ARG* 3.1 32.4 + - - +
80F LEU* 3.9 13.6 - - - +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E TYR* 4.1 13.9 - - + -
104E PHE* 4.1 4.5 - - + -
7F ALA 3.1 17.0 + - - +
8F ILE* 3.0 10.5 + - - +
10F GLY* 1.3 77.2 - - - +
12F LEU* 1.3 58.9 + - - +
13F ARG* 3.3 7.3 + - - +
14F LYS* 4.5 4.7 + - - +
15F GLY 4.8 0.7 - - - +
17F LEU* 3.3 25.4 - - + +
22F ILE* 4.1 22.9 - - + +
25F TYR* 3.8 35.1 - - + -
26F PHE* 3.9 29.4 - - + -
30F LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 3.2 33.5 + - + +
9F LEU* 3.9 10.1 - - + +
10F GLY 3.2 0.8 - - - -
11F LEU* 1.3 75.9 - - - +
13F ARG* 1.3 61.4 + - - +
14F LYS 3.2 4.8 + - - -
15F GLY* 3.4 18.8 + - - +
17F LEU* 3.8 31.4 - - + +
22F ILE* 4.5 8.3 - - + -
45F LEU* 5.5 1.1 - - + -
54F ILE* 4.9 10.3 - - + -
70F TYR* 4.0 40.8 - - + +
71F THR* 4.9 3.0 - - - +
72F LEU* 3.8 31.0 + - + +
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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