Contacts of the helix formed by residues 3 - 21 (chain B) in PDB entry 3ZWH
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 SER 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG 4.7 3.8 - - - -
41A GLU* 2.6 44.6 + - - -
43A PRO* 5.4 0.9 - - - -
1B MET 3.5 3.1 + - - -
2B ALA* 1.3 75.3 - - - +
4B PRO* 1.3 74.7 - - - +
5B LEU* 3.4 3.8 + - - +
6B GLU* 2.9 24.9 + - - +
7B LYS* 2.9 22.6 + - - +
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Residues in contact with PRO 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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11A VAL* 3.7 17.3 - - + +
15A THR* 5.4 1.8 - - - +
41A GLU* 4.7 6.1 - - - +
2B ALA 4.5 1.1 - - - +
3B SER* 1.3 87.7 - - - +
5B LEU* 1.3 55.9 + - - +
7B LYS* 3.4 4.7 + - + +
8B ALA* 2.9 27.7 + - - +
1100B AZI 3.6 38.7 + - - +
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Residues in contact with LEU 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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11A VAL* 3.8 5.5 - - - +
12A MET* 4.1 20.2 - - + +
15A THR* 4.0 26.9 + - + +
37A LEU* 4.1 11.4 - - + -
41A GLU* 4.2 7.1 + - + +
42A LEU* 3.7 29.6 - - + -
75A TYR* 3.9 16.8 - - - +
79A LEU* 3.9 32.5 - - + -
3B SER* 3.2 7.9 + - - +
4B PRO* 1.3 77.8 - - - +
6B GLU* 1.3 66.1 + - - +
8B ALA* 3.1 5.3 + - + +
9B LEU* 3.0 30.6 + - + +
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Residues in contact with GLU 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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41A GLU 3.4 19.1 - - - +
42A LEU* 3.5 10.4 - - + -
43A PRO* 3.3 13.3 - - - +
44A SER* 2.7 47.7 + - - +
45A TRP* 5.6 0.9 - - + -
1B MET 4.4 0.9 - - - +
2B ALA* 3.5 15.1 - - + -
3B SER* 2.9 32.8 + - - +
5B LEU* 1.3 76.4 - - - +
7B LYS* 1.3 62.2 + - - +
9B LEU* 3.3 12.2 + - + +
10B ASP* 3.3 25.1 + - - -
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Residues in contact with LYS 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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1B MET 6.0 0.8 - - - +
2B ALA* 3.7 34.2 + - + +
3B SER 2.9 19.7 + - - +
4B PRO* 3.6 5.2 - - + +
6B GLU* 1.3 73.6 - - - +
8B ALA* 1.3 64.9 + - - +
10B ASP* 3.2 11.2 + - - +
11B VAL* 3.0 29.1 + - + +
1100B AZI 4.2 21.4 + - - +
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Residues in contact with ALA 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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8A ALA* 3.8 39.6 - - + +
11A VAL* 4.4 5.4 - - + -
12A MET* 4.7 4.7 - - + -
4B PRO 2.9 14.3 + - - +
5B LEU* 3.3 19.1 - - + +
7B LYS* 1.3 77.2 - - - +
9B LEU* 1.3 61.7 + - - +
11B VAL* 3.2 6.4 + - - +
12B MET* 3.1 25.9 + - - +
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Residues in contact with LEU 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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12A MET* 5.5 1.1 - - - -
42A LEU* 3.9 25.6 - - + -
45A TRP* 5.1 2.5 - - + +
79A LEU* 3.9 37.5 - - + +
82A ILE* 3.7 30.1 - - + -
83A ALA* 4.7 8.8 - - + +
86A SER* 5.6 4.3 - - - +
5B LEU* 3.0 15.5 + - + +
6B GLU* 3.6 11.0 - - + +
7B LYS 3.3 0.2 - - - -
8B ALA* 1.3 75.7 - - + +
10B ASP* 1.3 63.9 + - - +
12B MET* 3.3 26.9 + - - +
13B VAL* 3.3 25.3 + - - +
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Residues in contact with ASP 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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86A SER* 5.1 10.7 + - - -
6B GLU 3.3 12.0 + - - +
7B LYS* 3.2 14.4 + - - +
9B LEU* 1.3 78.5 - - - +
11B VAL* 1.3 59.9 + - + +
13B VAL* 3.3 7.6 + - - +
14B SER* 2.9 32.7 + - - -
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Residues in contact with VAL 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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4A PRO* 3.8 18.2 - - + +
5A LEU* 3.8 31.9 - - + +
8A ALA* 4.1 7.6 - - + -
7B LYS* 3.0 17.5 + - + +
8B ALA* 3.2 10.1 + - - +
10B ASP* 1.3 75.0 - - + +
12B MET* 1.3 65.7 + - - +
14B SER* 3.5 7.4 - - - +
15B THR* 2.8 43.1 + - - +
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Residues in contact with MET 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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5A LEU* 4.3 9.2 - - + -
8A ALA* 5.4 2.0 - - + -
9A LEU* 5.4 1.6 - - + -
12A MET* 4.2 24.0 - - + +
79A LEU* 5.0 1.1 - - + +
80A SER* 4.7 11.9 - - - +
83A ALA* 4.0 13.0 - - + -
8B ALA 3.1 15.7 + - - +
9B LEU* 3.4 35.0 - - - +
11B VAL* 1.3 76.2 - - - +
13B VAL* 1.3 63.3 + - - +
16B PHE* 3.4 4.3 + - - +
72B PHE* 4.3 0.9 - - + -
75B TYR* 2.8 34.8 + - + -
76B CYS* 4.0 23.8 - - - -
79B LEU* 3.8 33.2 - - + -
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.8 25.4 - - + +
86A SER* 4.1 14.8 - - - +
87A ASN* 3.9 18.2 - - - +
90A PHE* 3.8 33.2 - - + -
9B LEU 3.3 15.1 + - - +
10B ASP* 3.7 9.2 - - - +
11B VAL 3.2 0.4 - - - -
12B MET* 1.3 74.1 - - - +
14B SER* 1.3 65.9 + - - +
16B PHE* 3.3 8.7 + - - +
17B HIS* 3.2 22.9 - - + -
72B PHE* 3.9 15.0 - - + -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 5.0 9.6 - - - -
10B ASP 2.9 19.8 + - - -
11B VAL* 3.4 11.3 + - - +
13B VAL* 1.3 79.6 - - - +
15B THR* 1.3 61.2 + - - +
17B HIS* 3.4 5.4 + - - +
18B LYS* 3.0 27.4 + - - +
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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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4A PRO* 5.5 1.4 - - - +
5A LEU* 4.0 21.1 + - + +
11B VAL* 2.8 36.0 + - - +
14B SER* 1.3 75.6 + - - +
16B PHE* 1.3 67.7 + - - +
18B LYS* 3.3 14.3 + - + +
19B TYR* 3.3 15.8 - - + -
37B LEU* 3.8 8.2 - - + +
41B GLU* 3.6 37.4 + - + +
75B TYR* 4.1 6.7 - - - -
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Residues in contact with PHE 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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91A GLU* 4.7 0.2 - - - -
12B MET 3.4 13.1 + - - +
13B VAL 3.3 9.1 + - - +
14B SER 3.3 0.4 - - - -
15B THR* 1.3 78.5 - - - +
17B HIS* 1.3 77.4 + + - +
19B TYR* 3.2 5.0 + - - +
20B SER* 2.9 38.5 + - - -
27B PHE 3.4 26.9 - - - -
28B LYS* 4.1 1.6 - - - -
29B LEU* 3.5 33.2 - - + +
37B LEU* 4.1 7.9 - - - -
70B VAL 3.7 14.1 - - - -
72B PHE* 3.6 38.4 - + + -
75B TYR* 3.5 33.9 + + + -
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Residues in contact with HIS 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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87A ASN* 2.6 27.5 + - - -
90A PHE* 3.3 40.1 - + + -
91A GLU* 3.1 34.1 + - + -
13B VAL* 3.2 26.2 + - + +
14B SER 3.4 3.1 + - - +
15B THR 3.3 0.4 - - - -
16B PHE* 1.3 89.3 - + - +
18B LYS* 1.3 65.8 + - - +
19B TYR 3.0 2.5 + - - -
20B SER* 3.2 16.1 + - - -
21B GLY* 3.5 16.6 + - - +
26B LYS 4.1 4.6 + - - -
27B PHE* 4.0 10.4 - + - -
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Residues in contact with LYS 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 SER 3.0 14.1 + - - +
15B THR* 3.3 16.6 - - + +
16B PHE 3.2 0.2 - - - -
17B HIS* 1.3 77.8 - - - +
19B TYR* 1.3 83.3 + - + +
21B GLY 5.0 0.2 + - - -
22B LYS* 3.8 19.6 - - - +
41B GLU* 2.9 26.1 + - - +
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Residues in contact with TYR 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 3.3 15.5 - - - -
16B PHE 3.2 2.0 + - - +
18B LYS* 1.3 103.0 + - + +
20B SER* 1.3 64.5 + - - +
21B GLY 3.2 2.5 + - - -
22B LYS* 3.3 19.7 + - - +
29B LEU* 3.9 11.2 - - + -
33B GLU* 3.1 37.7 - - + +
36B GLU* 3.5 45.1 - - + -
37B LEU* 3.8 16.6 - - + -
40B ARG* 3.4 25.9 + - - +
41B GLU* 2.5 45.7 + - + -
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Residues in contact with SER 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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16B PHE* 2.9 30.7 + - - -
17B HIS* 3.2 24.8 + - - -
19B TYR* 1.3 78.4 - - - +
21B GLY* 1.3 58.0 + - - +
22B LYS 3.3 0.7 + - - -
23B GLU 3.6 0.3 - - - +
25B ASP 3.3 6.4 - - - +
26B LYS* 2.9 18.3 + - - -
28B LYS 3.5 20.4 - - - -
29B LEU* 3.5 7.5 - - - +
33B GLU* 3.2 2.8 - - - +
501B CA 2.4 26.2 - - - -
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Residues in contact with GLY 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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17B HIS 3.5 12.3 + - - -
18B LYS 5.7 0.4 - - - -
19B TYR 3.2 1.6 - - - -
20B SER* 1.3 78.8 + - - +
22B LYS* 1.3 61.3 + - - +
23B GLU 3.6 0.4 - - - -
26B LYS* 3.2 37.5 - - - +
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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
------------------------------------------------------------
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