Contacts of the strand formed by residues 146 - 151 (chain B) in PDB entry 1Z9N
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 HIS 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.6 15.0 - - + -
72B HIS 3.2 9.9 - - - +
73B GLU* 2.8 35.9 + - - -
74B LYS 3.9 4.5 - - - -
75B PRO* 4.0 0.7 - - - -
96B TRP* 3.2 41.5 + + - -
142B GLU 3.7 13.1 + - - -
143B VAL* 3.4 23.5 + - - +
144B LYS 3.4 16.1 + - - -
145B GLY* 1.3 82.4 + - - +
147B SER* 1.3 62.6 + - - +
175B VAL* 3.8 7.1 - - - +
176B ILE* 2.9 26.1 + - - +
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Residues in contact with SER 147 (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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71B ILE* 3.1 7.8 - - - +
72B HIS* 2.8 47.2 + - - +
74B LYS 2.8 22.7 + - - -
76B SER 3.8 15.9 - - - -
77B CYS* 4.6 0.9 - - - -
92B ALA* 3.4 6.9 - - - +
146B HIS* 1.3 76.5 - - - +
148B LEU* 1.3 59.6 + - - +
149B MET* 4.6 0.2 - - - +
173B CYS* 4.1 9.4 - - - -
174B GLY 3.4 11.4 - - - -
175B VAL* 4.6 0.4 - - - -
176B ILE* 4.0 5.2 - - - -
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Residues in contact with LEU 148 (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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27B VAL* 4.3 17.5 - - + -
29B VAL* 5.1 4.3 - - + +
44B VAL* 3.7 42.2 - - + -
46B ILE* 5.1 0.4 - - + -
55B PHE* 4.1 13.9 - - + -
69B PHE* 3.7 26.5 - - + -
70B HIS 3.7 7.9 - - - +
71B ILE* 4.3 6.7 - - + -
117B LEU* 3.8 22.0 - - + -
147B SER* 1.3 72.2 - - - +
149B MET* 1.3 58.3 + - - +
150B ILE* 5.3 2.2 - - + +
172B ALA 4.1 0.2 - - - +
173B CYS* 3.2 8.2 - - - -
174B GLY 2.8 38.5 + - - +
176B ILE* 4.0 10.9 - - + +
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Residues in contact with MET 149 (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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32B LEU* 4.6 1.6 - - - -
68B GLY 3.8 0.5 - - - +
69B PHE* 3.3 9.6 - - - -
70B HIS 2.8 32.6 + - - +
72B HIS* 3.4 27.6 - - + +
89B GLY* 3.7 11.4 - - - +
92B ALA* 3.3 34.8 - - + -
147B SER* 4.6 0.4 - - - +
148B LEU* 1.3 74.2 - - - +
150B ILE* 1.3 63.5 + - - +
151B HIS* 3.6 21.2 - - + +
170B ARG* 3.7 33.0 - - + +
172B ALA 3.7 13.5 - - - +
173B CYS* 3.7 21.3 - - - -
200B CU 3.9 1.6 - - - -
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Residues in contact with ILE 150 (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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29B VAL* 4.3 11.7 - - + -
44B VAL* 5.3 0.9 - - + -
59B LEU* 3.7 19.5 - - + -
62B LEU* 4.5 3.6 - - + -
67B HIS* 3.9 11.0 - - + -
68B GLY 3.3 4.0 - - - +
69B PHE* 3.8 21.3 - - + -
120B LEU* 3.6 31.6 - - + -
148B LEU* 5.3 3.1 - - + +
149B MET* 1.3 79.4 - - - +
151B HIS* 1.3 56.2 + - - +
170B ARG* 3.8 1.6 - - - -
171B MET* 2.8 55.3 + - + +
172B ALA* 2.8 33.2 + - + +
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Residues in contact with HIS 151 (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 HIS* 2.7 34.7 + - - +
68B GLY* 2.8 16.3 + - - +
70B HIS* 3.1 21.2 + + - -
72B HIS* 3.5 8.5 + + - -
95B HIS* 4.8 2.9 - - - -
149B MET* 3.6 7.1 - - + +
150B ILE* 1.3 79.4 - - - +
152B ALA* 1.3 53.8 + - - +
153B GLY 4.0 3.8 - - - +
164B LEU* 6.4 1.6 - - + -
167B GLY* 3.2 25.7 - - - +
168B GLY 2.9 25.2 + - - -
169B PRO 3.3 7.9 + - - -
170B ARG* 3.9 21.1 - - + +
171B MET* 3.9 3.5 - - - +
200B CU 2.0 31.9 - - - -
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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