Contacts of the helix formed by residues 3 - 19 (chain C) in PDB entry 4B86
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 PRO 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ASN* 1.4 86.8 - - + +
4C VAL* 1.3 53.8 + - - +
5C ASN 3.7 0.9 - - - -
6C ALA* 3.7 12.8 - - + -
7C THR* 2.7 28.6 + - - +
65C TYR* 3.3 23.5 - - - +
93C ASN* 3.4 18.6 - - - +
95C GLN* 3.7 29.0 + - + -
96C LEU* 3.7 27.6 - - + -
99C LEU* 4.0 6.7 - - + -
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Residues in contact with VAL 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 4.0 14.6 + - - +
241A GLN* 4.8 13.7 - - + +
2C ASN* 3.6 22.4 - - - +
3C PRO* 1.3 70.8 - - - +
5C ASN* 1.3 65.4 + - - +
7C THR* 3.0 6.2 + - - -
8C ALA* 3.0 29.5 + - + +
61C THR* 5.8 6.5 - - + -
63C GLN* 3.1 19.6 + - - +
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Residues in contact with ASN 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 1.3 80.8 - - - +
6C ALA* 1.3 57.6 + - - +
8C ALA* 3.2 7.3 + - - +
9C LEU* 2.9 43.4 + - + +
41C SER* 4.8 5.6 - - - -
62C CYS 5.6 0.6 + - - -
63C GLN* 3.0 37.4 + - - +
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Residues in contact with ALA 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PRO* 3.7 16.1 - - + -
4C VAL 3.3 0.6 - - - -
5C ASN* 1.3 79.6 - - - +
7C THR* 1.3 56.5 + - - +
9C LEU* 3.8 0.4 - - - -
10C TYR* 2.9 29.5 + - - +
38C PHE* 3.7 5.7 - - - -
41C SER* 3.7 22.8 - - - +
42C LEU* 3.8 20.9 - - + -
63C GLN* 4.6 0.8 + - - -
65C TYR* 5.3 2.0 - - + -
96C LEU* 4.6 0.4 - - + -
99C LEU* 3.6 20.6 - - + -
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Residues in contact with THR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 5.1 2.2 - - + -
237A GLN* 3.0 27.7 + - + +
232B LEU* 4.8 9.0 - - + -
236B GLN* 4.9 1.3 - - - +
3C PRO 2.7 18.8 + - - +
4C VAL 3.0 10.0 + - - -
6C ALA* 1.3 75.2 - - - +
8C ALA* 1.3 64.2 + - - +
10C TYR* 3.3 5.4 + - + +
11C ILE* 3.0 32.8 + - - +
95C GLN* 3.3 28.3 - - - +
99C LEU* 3.6 25.8 - - + -
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Residues in contact with ALA 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 5.3 0.6 - - - +
4C VAL* 3.0 20.0 + - + +
5C ASN* 3.5 7.6 - - - +
7C THR* 1.3 76.3 + - - +
9C LEU* 1.3 59.0 + - + +
11C ILE* 3.3 12.0 + - - +
12C SER* 3.0 30.6 + - - -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASN* 2.9 25.1 + - + +
6C ALA 3.9 0.7 - - - +
8C ALA* 1.3 73.7 - - + +
10C TYR* 1.3 61.0 + - - +
12C SER* 3.8 4.2 - - - +
13C ALA* 2.9 32.9 + - - +
34C LEU* 3.7 29.0 - - + +
37C TYR* 3.4 44.2 - - + +
38C PHE* 3.7 21.6 - - + +
41C SER* 4.0 11.4 - - - +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 3.9 10.1 - - + -
233A ILE* 5.1 1.8 - - + -
225B ILE* 3.9 13.2 - - - +
229B GLN* 3.3 34.6 + - + +
232B LEU* 4.7 9.6 - - + -
6C ALA 2.9 18.9 + - - +
7C THR* 3.3 5.8 + - + +
9C LEU* 1.3 74.8 - - - +
11C ILE* 1.3 62.4 + - + +
14C SER* 2.9 52.0 + - - -
38C PHE* 3.3 33.8 - + + -
99C LEU* 4.0 19.5 - - + -
102C CYS* 3.4 49.5 - - + +
106C LEU* 4.7 5.2 - - + -
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 4.0 25.3 - - + +
233A ILE* 4.3 14.1 - - + +
234A GLU* 3.8 38.8 - - + +
237A GLN* 4.9 5.2 - - + -
7C THR* 3.0 27.0 + - - +
8C ALA* 3.6 9.4 - - - +
10C TYR* 1.3 79.0 - - + +
12C SER* 1.3 59.0 + - - +
14C SER* 3.9 0.7 - - - -
15C ARG* 2.9 69.9 + - - +
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA 3.0 18.3 + - - -
9C LEU* 3.8 5.1 - - - +
10C TYR 3.4 0.2 - - - -
11C ILE* 1.3 78.1 - - - +
13C ALA* 1.3 57.7 + - - +
15C ARG* 3.3 5.1 + - - +
16C LEU* 3.0 38.6 + - - +
34C LEU* 3.6 27.8 - - - +
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Residues in contact with ALA 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 2.9 21.0 + - - +
10C TYR 4.1 1.8 - - - +
12C SER* 1.3 72.3 - - - +
14C SER* 1.3 58.6 + - - +
16C LEU* 3.3 3.4 + - - +
17C VAL* 2.9 35.5 + - - +
31C ILE* 6.4 1.1 - - - -
34C LEU* 3.4 16.3 - - + +
35C LEU* 4.1 16.8 - - + -
38C PHE* 4.0 23.8 - - + -
106C LEU* 4.3 6.3 - - + -
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.6 26.2 - - - +
225B ILE* 5.0 0.9 - - - +
229B GLN* 4.6 1.6 + - - -
10C TYR* 2.9 36.9 + - - -
13C ALA* 1.3 75.8 - - - +
15C ARG* 1.3 56.4 + - - +
17C VAL 4.6 0.2 - - - +
18C LEU* 2.9 41.5 + - - +
106C LEU* 3.1 29.7 - - - +
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 4.7 11.9 - - + -
230A LEU* 3.6 16.6 + - + +
231A ASP* 2.7 43.5 + - - +
234A GLU* 2.9 43.4 + - - +
11C ILE* 2.9 36.3 + - - +
12C SER* 3.7 6.3 - - - +
14C SER* 1.3 77.7 - - - +
16C LEU* 1.3 65.0 + - + +
18C LEU 4.1 0.2 - - - -
19C ASN* 3.2 36.6 + - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER* 3.0 22.8 + - - +
13C ALA* 3.8 3.8 - - - +
15C ARG* 1.3 79.6 - - + +
17C VAL* 1.3 65.2 + - - +
19C ASN* 3.6 3.0 + - - -
20C TYR* 3.4 16.5 + - - -
27C ALA* 5.5 2.3 - - + +
30C GLU* 4.0 42.6 - - + +
31C ILE* 3.5 30.8 - - + +
34C LEU* 3.9 22.0 - - + -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 2.9 23.5 + - + +
14C SER* 4.1 4.5 - - - +
16C LEU* 1.3 75.5 - - - +
18C LEU* 1.3 60.1 + - + +
20C TYR* 3.3 25.8 - - + +
31C ILE* 4.0 27.6 - - + -
35C LEU* 5.4 1.3 - - + -
106C LEU* 4.6 12.8 - - + -
109C TYR* 4.0 27.7 - - + -
110C ILE* 3.8 41.5 - - + -
113C THR* 5.3 2.6 - - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LYS* 3.8 39.5 - - + +
226A LEU* 3.6 41.3 - - + -
227A LEU* 3.7 32.0 - - + +
230A LEU* 4.4 8.5 - - + -
222B LEU* 4.3 6.7 - - + -
229B GLN* 5.6 0.2 - - - +
14C SER* 2.9 32.5 + - - +
17C VAL* 1.3 79.4 - - + +
19C ASN* 1.3 61.4 + - - +
20C TYR 3.3 4.1 + - - -
106C LEU* 5.6 3.4 - - + -
109C TYR* 4.6 14.6 - - + -
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 3.6 27.8 - - - +
15C ARG* 3.2 25.1 + - - +
16C LEU* 3.8 4.5 - - - +
17C VAL 3.4 0.2 - - - -
18C LEU* 1.3 81.6 - - - +
20C TYR* 1.3 64.3 + - - +
21C ASP* 3.2 8.3 + - - +
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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
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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