Contacts of the helix formed by residues 87 - 97 (chain B) in PDB entry 3LZK
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 TYR 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 3.2 4.2 - - - -
86B ALA* 1.3 76.3 - - - +
88B VAL* 1.3 58.8 - - - +
89B ASN* 2.8 13.0 + - + +
90B HIS* 2.8 18.6 + - + +
91B VAL* 4.0 1.7 + - - +
142B ALA* 6.0 0.7 - - - +
233B ALA* 2.7 35.1 + - - +
235B ILE 3.5 10.1 - - - -
236B ASP 3.3 23.8 - - - +
237B MSE 3.3 32.7 - - + +
238B THR* 4.1 0.2 - - - -
262B SER* 4.0 17.5 + - - -
263B GLY 3.6 17.7 - - - -
264B THR 3.1 24.7 + - - +
265B VAL* 3.7 21.2 - - + +
266B SER* 3.5 26.5 - - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 4.0 9.4 - - - +
87B TYR* 1.3 70.3 - - - +
89B ASN* 1.3 63.9 + - - +
90B HIS 3.1 0.2 - - - -
91B VAL* 2.9 24.6 + - + +
92B GLU* 2.9 8.7 + - - +
102B MSE 3.6 33.7 - - + -
106B PHE* 3.3 26.0 - - + +
107B TRP* 3.5 21.5 - - + -
111B LEU* 6.5 0.2 - - + -
238B THR* 3.1 25.7 - - + +
239B PHE* 3.8 12.8 - - + -
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR 2.8 3.9 + - - +
88B VAL* 1.3 77.6 - - - +
90B HIS* 1.3 60.6 + - - +
92B GLU* 3.3 10.7 + - - +
93B LEU* 3.1 44.0 + - - +
107B TRP* 4.3 8.4 - - + -
236B ASP* 4.9 13.2 - - + +
238B THR* 4.6 1.2 - - - +
266B SER* 2.9 26.8 + - - +
267B ASN 3.9 3.8 + - - +
268B LYS* 3.3 55.1 - - + +
272B GLY 5.1 1.8 + - - +
273B PRO* 6.0 1.2 - - - +
289B GLU* 4.2 0.6 + - - -
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 5.6 4.3 - - - -
87B TYR* 2.8 12.6 + - + +
89B ASN* 1.3 78.0 - - - +
91B VAL* 1.3 73.1 + - + +
93B LEU* 3.1 9.8 + - + +
94B VAL* 3.1 35.7 + - + +
139B GLU* 4.7 6.8 + - - -
174B ARG* 5.6 2.4 + - - -
264B THR* 3.5 26.1 - - + +
266B SER* 4.0 9.8 + - - -
286B CYS* 3.6 27.1 - - - -
288B ALA* 4.8 5.6 - - + +
289B GLU* 2.9 38.4 + - + +
292B MSE 5.9 0.2 - - + -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PHE* 5.8 1.3 - - + -
85B SER* 4.0 20.2 - - - +
87B TYR 4.6 1.8 - - - +
88B VAL* 2.9 22.4 + - + +
90B HIS* 1.3 83.2 - - + +
92B GLU* 1.3 62.0 + - - +
94B VAL* 3.3 6.7 + - - +
95B ARG* 3.0 57.1 + - - +
102B MSE 3.7 17.3 - - - -
106B PHE* 4.2 4.3 - - + -
111B LEU* 3.9 25.8 - - + -
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Residues in contact with GLU 92 (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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88B VAL 2.9 11.9 + - - +
89B ASN* 3.4 21.5 - - - +
90B HIS 3.2 0.2 - - - -
91B VAL* 1.3 76.0 - - - +
93B LEU* 1.3 62.8 + - + +
95B ARG* 3.5 2.1 + - - +
96B LYS* 2.9 38.4 + - + +
102B MSE 3.6 29.4 - - + -
107B TRP* 4.2 19.2 - - + -
268B LYS* 4.0 15.0 + - - -
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Residues in contact with LEU 93 (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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89B ASN* 3.1 39.3 - - - +
90B HIS* 3.1 9.3 + - + +
92B GLU* 1.3 84.1 - - - +
94B VAL* 1.3 62.8 + - - +
96B LYS* 3.7 23.5 - - - +
97B ALA* 3.1 24.9 + - - +
272B GLY* 5.9 1.6 - - - -
273B PRO* 5.0 11.4 - - + -
274B GLY 5.8 0.4 - - - +
289B GLU* 3.7 31.4 - - + +
292B MSE 4.0 12.5 - - + +
293B ILE* 3.5 34.1 - - + -
296B ILE* 5.8 1.0 - - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 3.1 32.4 + - + +
91B VAL* 3.7 8.3 - - - +
93B LEU* 1.3 76.0 - - - +
95B ARG* 1.3 82.2 + - - +
97B ALA* 3.7 2.8 + - - +
98B ARG* 2.9 39.2 + - - +
288B ALA* 5.9 3.6 - - + -
292B MSE 4.0 27.7 - - + +
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Residues in contact with ARG 95 (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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183A LYS 4.5 8.3 + - - -
185A PHE* 4.6 18.6 - - - -
91B VAL* 3.0 28.9 + - - +
92B GLU 3.7 5.2 - - - +
94B VAL* 1.3 90.8 - - - +
96B LYS* 1.3 51.6 + - - +
98B ARG* 2.8 43.3 + - - +
99B ASN 2.8 29.8 + - - -
100B ALA* 3.2 29.0 + - + +
101B GLU 5.6 0.9 - - - -
102B MSE 3.6 23.2 - - + +
103B PRO* 5.8 1.7 - - - +
106B PHE* 3.4 34.2 - - - -
111B LEU* 5.0 1.2 - - - +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 2.9 25.3 + - + +
93B LEU* 3.7 29.0 - - - +
94B VAL 3.3 0.4 - - - -
95B ARG* 1.3 72.7 - - - +
97B ALA* 1.3 58.6 + - - +
98B ARG 3.0 5.2 - - - -
99B ASN* 2.9 29.0 + - - +
100B ALA 4.3 5.4 + - - +
272B GLY* 5.3 3.8 - - - -
273B PRO* 4.7 19.4 - - - +
293B ILE* 5.8 0.6 - - - +
296B ILE* 4.1 37.1 - - + +
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Residues in contact with ALA 97 (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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93B LEU 3.1 17.0 + - - +
94B VAL 4.0 1.8 - - - +
95B ARG 3.4 0.4 - - - -
96B LYS* 1.3 75.9 - - - +
98B ARG* 1.3 58.3 + - + +
99B ASN* 4.8 4.4 + - - -
292B MSE 3.7 43.1 - - - +
295B THR* 4.4 19.4 - - + +
296B ILE* 4.7 11.6 - - + +
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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