Contacts of the helix formed by residues 2 - 18 (chain C) in PDB entry 4PCW
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C SER* 1.3 76.8 - - - +
3C LEU* 1.3 64.2 + - - +
4C LEU* 3.8 8.5 + - - +
5C GLU* 2.8 39.9 + - - +
6C ASN* 2.8 27.6 + - - +
13D LEU* 5.4 0.7 - - - -
38D LYS* 5.5 8.7 - - - +
39D GLU* 3.3 19.5 - - - +
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Residues in contact with LEU 3 (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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2C THR* 1.3 71.4 - - - +
4C LEU* 1.3 63.5 + - + +
6C ASN* 3.2 10.1 + - - +
7C ILE* 3.1 28.5 + - + +
10D ILE* 4.0 27.8 - - + -
13D LEU* 3.6 28.1 - - + +
35D LEU* 4.9 3.6 - - + -
39D GLU* 2.7 23.5 + - + +
40D PHE* 4.1 26.9 - - + -
73D PHE* 4.3 13.2 - - + -
76D MET* 4.6 5.2 - - - -
77D VAL* 4.3 22.7 - - + -
80D LEU* 4.4 8.7 - - + -
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Residues in contact with LEU 4 (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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2C THR* 3.2 8.1 + - - +
3C LEU* 1.3 77.1 - - + +
5C GLU* 1.3 59.9 + - + +
7C ILE* 3.2 13.2 + - + +
8C PHE* 2.9 53.3 + - + -
39D GLU 3.5 23.8 - - - +
40D PHE* 4.2 27.1 - - + -
80D LEU* 4.8 4.3 - - + -
84D TYR* 4.1 32.8 - - + +
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Residues in contact with GLU 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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1C SER* 3.4 18.8 + - - +
2C THR* 2.8 45.6 + - - +
3C LEU 3.3 0.4 - - - -
4C LEU* 1.3 78.2 - - + +
6C ASN* 1.3 58.2 + - - +
8C PHE* 3.4 10.3 + - + +
9C ALA* 2.9 30.7 + - - +
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Residues in contact with ASN 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 3.8 19.1 + - - +
2C THR 2.8 19.8 - - - +
3C LEU* 3.2 11.0 + - - +
5C GLU* 1.3 76.1 - - - +
7C ILE* 1.3 59.4 + - - +
9C ALA* 3.3 2.6 + - - +
10C ILE* 3.0 36.0 + - - +
6D ASN* 3.7 22.8 + - - +
9D ALA* 3.4 35.3 - - - +
10D ILE* 4.0 22.6 - - + +
13D LEU* 5.5 1.4 - - - +
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Residues in contact with ILE 7 (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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3C LEU* 3.1 22.4 + - + +
4C LEU* 3.5 15.3 - - + +
6C ASN* 1.3 75.6 - - + +
8C PHE* 1.3 67.1 + - + +
10C ILE* 3.2 9.7 + - + +
11C ILE* 2.9 33.1 + - + +
10D ILE* 5.3 1.6 - - + -
77D VAL* 4.2 26.0 - - + +
80D LEU* 3.5 43.7 - - + +
81D ALA* 3.8 28.0 - - + +
84D TYR* 4.7 7.2 - - + -
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Residues in contact with PHE 8 (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 LEU* 2.9 44.0 + - + +
5C GLU* 3.8 8.5 - - + +
7C ILE* 1.3 75.9 - - + +
9C ALA* 1.3 57.4 + - - +
11C ILE* 3.3 13.9 + - + +
12C ASN* 2.9 45.2 + - - +
84D TYR* 3.6 48.9 - + + -
88D THR* 4.9 11.9 - - + -
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Residues in contact with ALA 9 (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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5C GLU 2.9 18.0 + - - +
6C ASN 3.5 2.9 - - - +
8C PHE* 1.3 77.6 - - - +
10C ILE* 1.3 56.6 + - - +
12C ASN* 3.5 5.5 + - - +
13C LEU* 2.9 32.4 + - - +
1D SER* 4.8 11.2 - - - +
6D ASN* 3.3 28.8 + - - +
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASN 3.0 22.8 + - - +
7C ILE* 3.2 8.3 + - + +
9C ALA* 1.3 73.6 - - - +
11C ILE* 1.3 65.4 + - - +
13C LEU* 3.7 5.8 - - - +
14C PHE* 3.1 22.2 + - - +
70C PHE* 4.5 3.1 - - + -
73C PHE* 3.9 23.2 - - + -
74C LEU* 4.2 19.1 - - + -
77C VAL* 4.7 15.7 - - + -
78C PHE* 5.8 3.4 - - + -
3D LEU* 4.2 14.8 - - + -
6D ASN* 3.8 23.1 - - + +
7D ILE 5.2 0.7 - - - +
10D ILE* 3.9 26.5 - - + -
77D VAL* 6.0 0.4 - - + -
81D ALA* 5.8 1.8 - - + -
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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
----------------------------------------------------------
7C ILE* 2.9 35.2 + - + +
8C PHE* 3.6 14.1 - - + +
10C ILE* 1.3 76.6 - - - +
12C ASN* 1.3 59.8 + - - +
14C PHE* 3.4 3.5 + - - +
15C LYS* 3.1 30.5 + - - +
70C PHE* 3.7 25.8 - - + -
81D ALA* 3.6 19.7 - - + +
84D TYR* 3.7 22.4 - - + +
85D TYR* 3.7 20.5 - - + +
88D THR* 4.0 26.0 - - + +
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Residues in contact with ASN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 2.9 31.9 + - - +
9C ALA* 4.1 5.6 - - - +
11C ILE* 1.3 76.0 - - - +
13C LEU* 1.3 65.8 + - - +
15C LYS* 3.5 9.6 + - - +
16C GLN* 3.0 27.8 + - - +
88D THR* 4.1 21.8 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA 2.9 19.0 + - - +
10C ILE* 3.7 6.5 - - - +
12C ASN* 1.3 76.8 - - - +
14C PHE* 1.3 62.4 + - - +
16C GLN* 3.2 13.6 + - + +
17C TYR* 3.2 30.1 + - + -
35C LEU* 6.0 1.3 - - + -
39C GLU* 3.6 26.7 - - + +
73C PHE* 5.5 3.8 - - + -
1D SER 3.6 22.7 - - - +
2D THR* 4.4 0.7 - - - -
3D LEU* 3.6 44.0 - - + +
6D ASN* 5.2 2.9 - - - +
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Residues in contact with PHE 14 (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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10C ILE 3.1 13.8 + - - +
11C ILE 3.7 4.0 - - - +
13C LEU* 1.3 78.6 - - - +
15C LYS* 1.3 63.8 + - - +
17C TYR* 3.2 8.1 + - - +
18C SER* 2.8 36.9 + - - -
25C ASP 3.7 18.2 - - - -
26C THR* 4.1 2.2 - - - -
27C LEU* 3.4 32.7 - - + +
35C LEU* 5.1 1.3 - - + -
68C ILE 3.5 19.1 - - - -
70C PHE* 3.5 36.3 - + + -
73C PHE* 3.4 45.7 - + + -
85D TYR* 3.9 17.3 - + - -
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Residues in contact with LYS 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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11C ILE* 3.1 23.3 + - + +
12C ASN* 3.8 10.5 - - - +
13C LEU 3.3 0.2 - - - -
14C PHE* 1.3 76.2 - - - +
16C GLN* 1.3 63.6 + - - +
18C SER* 3.2 15.2 + - - +
19C LYS* 3.3 25.1 + - + +
24C THR 4.8 2.9 - - - +
25C ASP* 5.5 1.6 - - - -
85D TYR* 3.4 45.7 + - + +
88D THR* 2.3 49.3 + - - +
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Residues in contact with GLN 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 ASN* 3.0 19.4 + - - +
13C LEU* 3.5 9.2 - - + +
14C PHE 3.1 0.6 - - - -
15C LYS* 1.3 81.3 - - - +
17C TYR* 1.3 64.3 + - + +
19C LYS* 3.5 46.6 + - - +
20C LYS 4.8 0.3 + - - -
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Residues in contact with TYR 17 (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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13C LEU* 3.2 32.7 + - + -
14C PHE 3.2 4.5 + - - +
16C GLN* 1.3 79.9 - - + +
18C SER* 1.3 59.0 + - - +
19C LYS 3.3 2.6 + - - -
20C LYS* 3.9 5.2 + - - +
27C LEU* 3.8 17.3 - - + -
31C GLU* 3.2 29.7 - - - +
34C GLU* 3.8 20.3 - - + +
35C LEU* 3.6 50.9 - - + -
38C LYS* 3.1 34.3 - - - +
39C GLU* 2.7 31.0 + - + -
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 2.8 27.6 + - - -
15C LYS* 3.2 11.8 + - - -
17C TYR* 1.3 75.1 - - - +
19C LYS* 1.3 55.7 + - - +
23C ASN 3.0 9.2 - - - +
24C THR* 3.0 20.4 + - - -
26C THR 3.2 26.0 - - - -
27C LEU* 3.7 10.1 - - - -
31C GLU* 3.3 9.0 - - - -
102C CA 2.4 23.4 - - - -
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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