Contacts of the helix formed by residues 2 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.3 1.6 - - - -
38A LYS 5.5 2.2 - - - +
39A GLU* 3.5 28.5 - - - +
1B SER* 1.3 76.1 - - - +
3B LEU* 1.3 63.9 + - - +
4B LEU* 3.5 6.2 + - - +
5B GLU* 3.1 31.5 + - + +
6B ASN* 2.9 29.2 + - - -
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Residues in contact with LEU 3 (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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10A ILE* 3.8 37.7 - - + -
13A LEU* 3.6 28.2 - - + +
39A GLU* 3.6 8.2 + - - +
40A PHE* 3.2 43.3 - - + -
73A PHE* 4.3 7.0 - - + -
76A MET* 5.7 0.4 - - - -
77A VAL* 4.1 23.8 - - + -
80A LEU* 5.3 4.7 - - + -
2B THR* 1.3 74.5 - - - +
4B LEU* 1.3 58.4 + - - +
6B ASN* 3.1 5.7 + - - +
7B ILE* 2.9 41.2 + - + +
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Residues in contact with LEU 4 (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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39A GLU 4.4 8.6 + - - +
40A PHE* 5.2 7.6 - - + +
43A ILE* 3.6 37.7 - - + -
80A LEU* 5.6 3.1 - - + -
84A TYR* 3.6 39.7 - - + +
2B THR* 3.3 7.9 + - - +
3B LEU* 1.3 79.7 - - - +
5B GLU* 1.3 60.9 + - + +
7B ILE* 3.9 13.0 - - + +
8B PHE* 3.2 43.0 + - + -
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Residues in contact with GLU 5 (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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6A ASN* 5.2 0.2 - - - -
1B SER* 4.5 11.9 - - - -
2B THR* 3.1 32.6 + - + +
3B LEU 3.2 0.4 - - - -
4B LEU* 1.3 78.5 - - + +
6B ASN* 1.3 56.6 + - - +
8B PHE* 3.4 5.5 + - - +
9B ALA* 2.9 28.4 + - - +
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Residues in contact with ASN 6 (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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6A ASN* 2.7 39.2 + - + +
9A ALA* 3.2 35.2 + - - +
10A ILE* 4.2 17.1 - - + +
13A LEU* 5.5 1.2 - - - +
1B SER* 3.7 15.4 + - - -
2B THR 2.9 22.0 + - - -
3B LEU* 3.1 9.8 + - - +
5B GLU* 1.3 75.8 - - - +
7B ILE* 1.3 65.6 + - - +
9B ALA* 3.3 2.3 + - - +
10B ILE* 3.1 30.0 + - - +
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Residues in contact with ILE 7 (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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10A ILE* 5.4 1.6 - - + -
77A VAL* 3.9 33.0 - - + +
80A LEU* 4.2 19.7 - - + -
81A ALA* 3.5 33.3 - - + +
84A TYR* 4.7 7.6 - - + -
3B LEU* 2.9 43.4 + - + +
4B LEU* 3.9 13.5 - - + +
6B ASN* 1.3 77.0 - - + +
8B PHE* 1.3 60.4 + - + +
10B ILE* 3.2 11.5 + - + +
11B ILE* 3.0 32.6 + - + +
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Residues in contact with PHE 8 (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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84A TYR* 3.6 52.5 - + + -
87A SER 6.1 4.3 - - - -
4B LEU* 3.2 39.3 + - + +
5B GLU* 3.8 5.2 - - - +
7B ILE* 1.3 79.4 - - + +
9B ALA* 1.3 61.2 + - - +
11B ILE* 3.3 15.9 + - + +
12B ASN* 2.8 50.3 + - - +
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Residues in contact with ALA 9 (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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1A SER* 5.2 5.6 - - - +
6A ASN* 3.4 33.2 - - - +
5B GLU 2.9 18.3 + - - +
6B ASN 3.5 1.1 - - - +
7B ILE 3.2 0.2 - - - -
8B PHE* 1.3 77.4 - - - +
10B ILE* 1.3 56.2 + - - +
12B ASN* 3.8 5.9 - - - +
13B LEU* 2.9 30.4 + - - +
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Residues in contact with ILE 10 (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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3A LEU* 3.9 20.0 - - + -
6A ASN* 4.1 13.2 - - + +
7A ILE* 5.3 1.8 - - + -
10A ILE* 4.1 25.4 - - + -
77A VAL* 6.1 0.4 - - + -
78A PHE* 4.8 5.6 - - + -
81A ALA* 5.8 2.2 - - + -
6B ASN 3.1 17.0 + - - +
7B ILE* 3.2 11.9 + - + +
9B ALA* 1.3 75.3 - - - +
11B ILE* 1.3 62.1 + - - +
13B LEU* 3.5 8.9 + - - +
14B PHE* 3.2 21.0 + - - +
70B PHE* 4.8 1.8 - - + -
73B PHE* 3.7 23.5 - - + -
74B LEU* 4.2 16.2 - - + -
77B VAL* 4.2 19.5 - - + -
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Residues in contact with ILE 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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81A ALA* 3.5 21.5 - - + +
84A TYR* 3.7 23.8 - - + +
85A TYR* 3.9 27.6 - - + +
87A SER 6.5 0.7 - - - -
7B ILE* 3.0 28.4 + - + +
8B PHE* 3.3 21.7 + - + +
10B ILE* 1.3 76.8 - - - +
12B ASN* 1.3 65.5 + - - +
14B PHE* 3.2 6.2 + - - +
15B LYS* 3.1 34.9 + - + +
70B PHE* 3.6 23.9 - - + -
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Residues in contact with ASN 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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8B PHE* 2.8 42.9 + - - +
9B ALA* 4.0 5.6 - - - +
11B ILE* 1.3 74.6 - - - +
13B LEU* 1.3 63.6 + - - +
15B LYS* 3.8 23.2 + - - +
16B GLN* 3.1 26.7 + - - +
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Residues in contact with LEU 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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1A SER 5.1 5.2 - - - +
2A THR 4.8 1.6 - - - -
3A LEU* 3.7 24.7 - - + +
6A ASN* 5.7 0.9 - - - +
9B ALA 2.9 18.8 + - - +
10B ILE* 3.6 5.6 - - - +
11B ILE 3.2 0.2 - - - -
12B ASN* 1.3 74.7 - - - +
14B PHE* 1.3 62.9 + - - +
16B GLN* 3.3 16.1 - - - +
17B TYR* 3.3 30.4 - - + -
35B LEU* 3.9 19.3 - - + -
39B GLU* 3.3 39.0 - - + +
73B PHE* 3.4 33.4 - - + -
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Residues in contact with PHE 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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85A TYR* 3.5 31.9 - + - -
10B ILE 3.2 5.9 + - - +
11B ILE 3.2 7.4 + - - +
13B LEU* 1.3 83.9 - - - +
15B LYS* 1.3 60.6 + - - +
17B TYR 3.5 1.6 + - - -
18B SER* 3.0 43.8 + - - -
25B ASP 3.7 9.9 - - - -
26B THR* 4.1 5.2 - - - -
27B LEU* 3.3 38.3 - - + +
35B LEU* 4.8 3.6 - - - -
68B ILE 3.6 15.9 - - - -
69B ASP 3.9 10.3 - - - -
70B PHE* 3.5 42.0 - + + -
73B PHE* 3.7 22.2 - + + -
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Residues in contact with LYS 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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85A TYR* 4.3 24.7 + - + +
87A SER* 3.7 33.6 + - - +
11B ILE* 3.1 34.1 + - + +
12B ASN* 3.8 19.1 + - - +
13B LEU 3.2 0.4 - - - -
14B PHE* 1.3 73.2 - - - +
16B GLN* 1.3 65.1 + - - +
17B TYR 3.0 3.5 + - - -
18B SER* 3.2 9.1 + - - +
19B LYS* 3.1 36.9 + - + +
24B THR* 5.7 5.8 - - + +
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Residues in contact with GLN 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 ASN 3.1 13.2 + - - +
13B LEU* 3.3 25.5 - - - +
15B LYS* 1.3 76.2 - - - +
17B TYR* 1.3 89.0 + - + +
19B LYS* 4.2 22.4 - - - +
20B LYS* 3.7 23.0 - - - +
39B GLU* 5.6 0.9 - - - +
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Residues in contact with TYR 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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13B LEU* 3.3 22.0 - - + +
14B PHE 3.5 2.4 + - - +
15B LYS 3.0 0.4 - - - -
16B GLN* 1.3 108.8 + - + +
18B SER* 1.3 60.0 + - - +
19B LYS 3.3 2.8 + - - -
20B LYS* 3.6 17.0 + - + +
27B LEU* 3.6 17.9 - - + -
31B GLU* 2.9 47.0 - - - +
34B GLU* 3.6 37.7 - - + -
35B LEU* 3.9 30.5 - - + -
38B LYS* 3.4 30.5 - - - +
39B GLU* 4.4 12.7 + - - -
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Residues in contact with SER 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 PHE* 3.0 33.2 + - - -
15B LYS* 3.2 15.6 + - - +
17B TYR* 1.3 76.6 - - - +
19B LYS* 1.3 56.7 + - - +
20B LYS 3.3 1.3 - - - -
21B ASP* 3.3 0.9 - - - +
23B ASN 2.8 9.9 - - - +
24B THR 2.8 23.3 + - - -
26B THR 3.3 23.6 - - - -
27B LEU* 3.5 6.7 - - - +
31B GLU* 3.2 2.3 - - - +
101B CA 2.3 26.7 - - - -
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Residues in contact with LYS 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 LYS* 3.1 25.7 + - + +
16B GLN* 4.2 23.6 - - - +
17B TYR 3.3 0.2 - - - -
18B SER* 1.3 76.3 + - - +
20B LYS* 1.3 60.5 + - + +
21B ASP 3.1 13.5 + - - +
24B THR* 4.1 30.5 + - + +
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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