Contacts of the helix formed by residues 10 - 24 (chain B) in PDB entry 1CF5
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 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B THR 3.5 6.4 + - - +
9B ALA* 1.3 76.9 - - - +
11B ALA* 1.3 63.5 + - - +
12B LYS* 2.9 43.0 + - - +
13B THR* 3.0 21.1 + - + +
14B TYR* 3.0 11.6 + - - +
127B LEU* 4.4 1.6 - - - +
173B VAL* 4.4 8.7 - - - -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 1.3 74.1 - - - +
12B LYS* 1.3 63.9 + - - +
14B TYR* 4.3 5.6 - - - -
15B THR* 3.2 28.6 + - + +
170B ALA* 2.9 35.4 - - + +
171B LYS* 5.4 0.2 - - - -
173B VAL* 3.8 11.2 - - + +
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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
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10B THR* 2.9 35.6 + - - +
11B ALA* 1.3 77.5 - - - +
13B THR* 1.3 66.5 + - + +
15B THR* 3.1 11.1 + - - -
16B LYS* 3.1 25.9 + - + +
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.9 10.3 - - - -
8B THR* 3.9 14.4 - - - +
9B ALA* 3.4 9.5 - - - -
10B THR* 3.0 29.5 + - + +
12B LYS* 1.3 84.8 - - + +
14B TYR* 1.3 67.8 + - - +
16B LYS* 3.2 8.5 + - - +
17B PHE* 3.0 26.0 + - - +
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Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.8 26.5 - + + -
10B THR 3.0 12.8 + - - +
11B ALA* 3.9 6.1 - - - +
12B LYS 3.3 0.2 - - - -
13B THR* 1.3 82.6 + - - +
15B THR* 1.3 62.6 + - + +
17B PHE* 3.6 8.9 + + - +
18B ILE* 3.1 44.7 + - + +
127B LEU* 3.8 21.1 - - + -
130B LEU* 5.1 3.6 - - + -
155B THR 3.1 15.5 + - - -
159B ALA* 3.0 31.9 - - - +
166B GLU* 3.3 22.2 - - + -
169B VAL* 3.1 29.7 - - + +
170B ALA* 3.6 22.9 - - + -
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.2 15.0 + - + +
12B LYS* 3.1 12.8 + - - -
14B TYR* 1.3 79.1 - - + +
16B LYS* 1.3 56.9 + - - +
18B ILE* 3.1 7.7 + - - +
19B GLU* 2.8 28.6 + - - +
166B GLU* 3.4 27.6 - - + +
167B ARG* 5.9 1.3 - - + -
170B ALA* 3.7 25.8 - - + -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 3.1 14.8 + - + +
13B THR* 3.5 12.6 - - - +
15B THR* 1.3 73.9 + - - +
17B PHE* 1.3 55.0 + - - +
19B GLU* 2.8 33.0 + - - +
20B ASP* 2.7 61.7 + - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.4 20.4 - - + -
3B ASN 3.3 28.0 - - - +
4B PHE* 3.6 38.1 - + + -
13B THR 3.0 13.6 + - - +
14B TYR* 3.7 16.6 - + - -
16B LYS* 1.3 77.6 - - - +
18B ILE* 1.3 80.8 + - + +
20B ASP* 3.1 10.1 + - - +
21B PHE* 2.8 40.0 + + + +
50B LEU* 4.1 26.9 - - + -
52B LEU* 4.7 4.7 - - + -
130B LEU* 5.8 0.7 - - + -
156B THR* 4.3 15.9 - - + -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 3.1 47.0 + - + +
15B THR* 3.1 12.5 + - - +
17B PHE* 1.3 100.4 - - + +
19B GLU* 1.3 57.1 + - - +
21B PHE* 4.1 6.1 - - + +
22B ARG* 3.0 53.1 + - - +
155B THR 4.1 2.7 - - - +
156B THR 4.3 6.3 - - - +
159B ALA* 3.9 9.6 - - + -
160B ALA* 4.0 14.1 - - + +
166B GLU* 3.9 12.8 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR 2.8 10.8 + - - +
16B LYS* 2.8 33.8 + - + +
18B ILE* 1.3 76.7 - - - +
20B ASP* 1.3 67.1 + - - +
22B ARG* 4.1 11.1 - - - +
23B ALA* 3.0 30.6 + - + +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.8 16.9 - - + +
3B ASN 5.6 2.3 + - - +
16B LYS* 2.7 48.8 + - - +
17B PHE* 3.4 10.7 - - - +
19B GLU* 1.3 75.1 - - - +
21B PHE* 1.3 65.4 + - - +
23B ALA* 3.0 5.4 + - - +
24B THR* 2.9 33.1 + - + +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.8 15.0 - - + +
17B PHE* 2.8 34.6 + + + +
18B ILE* 4.1 7.4 - - + +
20B ASP* 1.3 74.8 - - - +
22B ARG* 1.3 63.2 + - - +
24B THR* 3.2 8.7 + - - -
25B LEU* 3.3 26.1 + - + +
48B ILE* 4.0 22.7 - - + -
50B LEU* 4.1 18.6 - - + -
64B ILE* 4.2 19.1 - - + -
69B VAL* 3.3 25.4 - - + -
156B THR 3.9 11.0 - - - -
157B ALA* 3.8 15.0 - - - -
160B ALA* 3.5 26.0 - - + -
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR 5.4 0.2 + - - -
18B ILE* 3.0 35.6 + - - +
19B GLU* 4.2 9.8 - - - +
20B ASP 3.4 0.2 - - - -
21B PHE* 1.3 77.4 - - - +
23B ALA* 1.3 61.0 + - - +
25B LEU* 3.3 30.4 + - - +
159B ALA 3.0 23.4 + - - -
160B ALA* 2.7 30.2 + - + +
163B LYS* 3.8 8.3 - - - +
166B GLU* 2.9 32.5 + - - +
236B LYS* 3.3 36.0 - - - +
237B LEU* 5.1 12.8 - - + +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 3.0 22.4 + - + +
20B ASP* 3.0 9.8 + - - +
22B ARG* 1.3 77.3 - - - +
24B THR* 1.3 62.5 + - + +
25B LEU 4.0 4.1 - - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.8 17.1 - - + +
20B ASP* 2.9 21.2 + - + +
21B PHE 3.2 1.4 + - - -
23B ALA* 1.3 79.4 - - + +
25B LEU* 1.3 65.3 + - - +
26B PRO* 3.2 10.0 - - - +
48B ILE* 2.9 37.0 - - - +
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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