Contacts of the helix formed by residues 57 - 71 (chain B) in PDB entry 1ZWS
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASP* 4.2 3.1 + - - +
221A THR* 4.2 5.2 - - - +
47B ARG* 3.0 32.3 - - - +
56B VAL* 1.3 75.9 - - - +
58B ARG* 1.3 58.2 + - - +
59B GLU* 3.1 21.1 + - - +
60B GLU* 2.9 31.3 + - - -
61B ILE* 2.8 32.7 + - - +
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Residues in contact with ARG 58 (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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3B PRO* 6.3 0.2 - - - +
4B PHE* 3.5 25.5 - - - -
46B LYS* 6.1 3.5 - - - +
56B VAL 3.7 1.2 + - - -
57B SER* 1.3 73.9 + - - +
59B GLU* 1.3 57.7 + - - +
61B ILE* 3.0 11.8 - - - +
62B GLU* 2.8 102.1 + - - +
84B GLU* 3.5 25.0 + - - -
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Residues in contact with GLU 59 (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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220A ASP* 5.9 0.7 - - - +
221A THR* 4.3 15.6 + - + +
223A GLN* 4.2 5.4 + - - +
57B SER* 3.1 9.5 + - - +
58B ARG* 1.3 74.6 - - - +
60B GLU* 1.3 58.9 + - - +
61B ILE 2.7 4.8 + - - -
62B GLU* 2.8 9.6 + - - -
63B ARG* 2.5 73.1 + - + +
166B HIS* 4.7 2.3 + - - -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP 4.1 4.0 - - - +
221A THR* 3.7 19.2 - - + +
222A LYS 5.1 1.2 + - - -
47B ARG* 4.1 2.1 + - - -
55B GLY 5.3 0.2 - - - +
56B VAL* 3.2 29.2 - - + +
57B SER* 2.9 29.2 + - - +
59B GLU* 1.3 78.4 - - - +
61B ILE* 1.3 63.8 + - - +
63B ARG* 3.0 35.1 - - - +
64B GLU* 3.2 20.4 + - - +
163B GLY* 4.7 8.7 - - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.4 14.4 - - + -
44B ILE* 3.1 44.2 - - + +
46B LYS* 5.3 2.7 - - + -
56B VAL* 3.7 15.0 - - + +
57B SER 2.8 30.0 + - - +
58B ARG* 3.0 17.3 - - - +
59B GLU 2.7 3.8 + - - -
60B GLU* 1.3 70.0 - - - +
62B GLU* 1.3 61.7 + - + +
64B GLU* 2.6 31.2 + - - +
65B VAL* 3.0 23.1 + - + +
89B VAL* 4.1 25.1 - - + -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.5 7.2 - - + -
58B ARG* 2.8 62.8 + - - +
59B GLU* 2.8 7.4 + - - +
61B ILE* 1.3 79.3 - - + +
63B ARG* 1.3 58.3 + - - +
65B VAL* 2.9 8.2 + - - -
66B SER* 2.6 39.2 + - - -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A THR* 4.7 3.6 - - - +
223A GLN* 2.9 31.1 - - - +
59B GLU* 2.5 45.8 + - + +
60B GLU* 3.0 40.5 + - - +
62B GLU* 1.3 71.3 - - - +
64B GLU* 1.3 51.8 - - - +
66B SER* 4.1 4.6 - - - -
67B ILE* 2.6 40.5 + - + +
163B GLY 5.3 3.0 + - - -
165B ALA 4.0 15.8 + - - +
166B HIS* 3.3 40.3 + - + -
167B GLU* 5.1 2.7 - - + +
174B PHE* 4.8 0.4 - - - -
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Residues in contact with GLU 64 (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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42B LYS* 2.6 35.7 + - - +
44B ILE* 4.0 17.1 - - + +
60B GLU 3.2 13.1 + - - +
61B ILE* 2.6 17.5 + - - +
63B ARG* 1.3 69.0 - - - +
65B VAL* 1.3 60.8 - - + +
67B ILE* 3.2 6.4 + - - +
68B LEU* 2.9 40.2 + - + +
91B LEU* 4.2 7.3 - - + +
93B LEU* 5.7 0.5 - - - +
162B PHE* 2.8 43.0 + - + +
163B GLY* 3.4 12.7 - - - +
165B ALA 5.3 0.9 - - - -
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Residues in contact with VAL 65 (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 23.6 - - + -
44B ILE* 6.0 1.1 - - + -
61B ILE* 3.0 22.4 + - + +
62B GLU* 2.9 7.7 + - - +
64B GLU* 1.3 73.8 - - + +
66B SER* 1.3 68.8 + - - +
67B ILE 3.0 0.3 + - - -
68B LEU* 3.1 9.9 + - - +
69B ARG* 2.9 55.0 + - - +
79B LEU* 4.4 3.4 - - + -
82B VAL* 4.3 10.3 - - + -
89B VAL* 5.6 0.4 - - + -
91B LEU* 4.0 26.0 - - + -
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Residues in contact with SER 66 (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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62B GLU* 2.6 23.5 + - - -
63B ARG* 4.1 5.8 - - - -
65B VAL* 1.3 75.5 - - - +
67B ILE* 1.3 66.5 + - - +
69B ARG* 3.2 12.0 + - - +
70B GLN* 3.2 34.1 + - - +
167B GLU* 4.8 2.3 + - - -
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Residues in contact with ILE 67 (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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63B ARG* 2.6 25.4 - - + +
64B GLU* 3.2 8.7 - - - +
65B VAL 3.0 0.2 - - - -
66B SER* 1.3 73.2 - - - +
68B LEU* 1.3 58.9 + - - +
69B ARG 2.9 1.3 - - - -
70B GLN* 2.6 34.4 + - - +
71B VAL* 3.3 10.6 + - + +
135B ILE* 3.9 35.9 - - + -
162B PHE* 3.9 26.5 - - + -
165B ALA* 4.1 10.1 - - + +
166B HIS* 4.0 4.7 - - - +
167B GLU* 3.7 40.2 - - + +
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Residues in contact with LEU 68 (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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64B GLU* 2.9 38.1 + - + +
65B VAL* 3.6 7.0 - - - +
67B ILE* 1.3 71.9 - - - +
69B ARG* 1.3 58.3 + - - +
71B VAL* 3.0 30.3 - - + +
77B ILE* 4.4 12.6 - - + +
79B LEU* 3.9 28.9 + - + +
91B LEU* 4.4 9.9 - - + -
93B LEU* 4.0 30.7 - - + -
162B PHE* 3.4 46.0 - - + +
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Residues in contact with ARG 69 (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 GLU* 3.1 44.8 + - - +
3B PRO 4.0 8.7 + - - -
4B PHE* 4.0 15.8 - - - +
65B VAL* 2.9 33.9 + - - +
66B SER* 3.3 13.5 - - - +
67B ILE 2.7 4.8 + - - -
68B LEU* 1.3 76.6 - - - +
70B GLN* 1.3 61.1 + - + +
71B VAL 3.3 5.2 + - - +
72B LEU* 5.4 1.7 - - - +
79B LEU* 3.9 16.7 - - + +
82B VAL* 4.3 11.9 + - - +
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Residues in contact with GLN 70 (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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66B SER* 3.2 27.6 + - - +
67B ILE* 2.6 17.3 + - - +
69B ARG* 1.3 73.0 - - + +
71B VAL* 1.3 59.2 + - - +
72B LEU* 4.8 1.0 - - - +
129B TYR* 3.5 2.1 + - - -
133B LYS* 3.1 52.7 + - + +
135B ILE* 4.2 20.5 - - + +
167B GLU* 2.9 30.0 + - - +
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Residues in contact with VAL 71 (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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67B ILE* 3.6 8.1 - - + +
68B LEU* 3.0 47.9 - - + +
69B ARG 3.8 3.3 - - - +
70B GLN* 1.3 78.4 - - - +
72B LEU* 1.3 67.4 + - - +
73B HIS 4.0 0.4 - - - -
76B VAL* 4.3 20.4 - - + -
77B ILE 4.5 4.4 - - - +
78B THR* 4.9 6.3 - - - +
129B TYR* 3.3 14.4 - - + -
130B LEU* 3.3 31.9 - - + -
133B LYS* 5.4 1.1 - - + -
135B ILE* 4.2 15.5 - - + -
162B PHE* 4.9 1.8 - - + -
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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