Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 3LZP
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 GLY 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ASN* 4.7 2.2 - - - -
76B ASP* 3.3 12.1 - - - -
111B GLY 3.3 4.0 + - - -
112B VAL* 1.3 78.4 - - - +
114B ASN* 1.3 64.5 + - - -
115B TYR* 3.4 8.8 - - - -
153B LYS* 3.6 3.9 - - - +
154B TYR 2.9 34.4 + - - +
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Residues in contact with ASN 114 (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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74B ASN* 3.5 6.4 - - - +
75B THR* 2.9 39.8 + - - +
76B ASP* 2.9 29.8 + - - +
113B GLY* 1.3 73.5 - - - -
115B TYR* 1.3 62.5 + - - +
152B PHE 3.7 4.8 - - - +
153B LYS* 2.9 39.6 + - - +
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Residues in contact with TYR 115 (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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72B LEU* 3.6 20.6 - - + -
73B LYS 3.2 21.1 - - - -
74B ASN* 3.1 28.6 + - + -
75B THR* 4.5 2.2 - - - +
102B MET* 3.6 15.5 - - + -
110B PHE* 2.9 32.7 + + - -
111B GLY 2.7 29.1 + - - -
113B GLY 3.4 17.0 - - - -
114B ASN* 1.3 74.1 - - - +
116B GLU* 1.3 63.1 + - - +
117B LEU 4.3 0.2 - - - -
151B LYS* 3.4 7.6 - - - +
152B PHE* 2.9 56.1 + + + +
154B TYR* 3.7 21.8 - - + -
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Residues in contact with GLU 116 (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 GLU 3.7 1.0 - - - +
72B LEU* 3.5 4.9 - - - +
73B LYS* 2.8 52.8 + - + +
75B THR* 3.6 26.0 - - + +
115B TYR* 1.3 75.0 - - - +
117B LEU* 1.3 60.8 + - - +
118B THR* 5.2 3.1 - - - +
149B ASP* 6.0 1.3 - - - +
150B TYR 3.3 4.9 - - - +
151B LYS* 3.8 38.8 + - + +
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Residues in contact with LEU 117 (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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6B ILE* 3.9 12.6 - - + -
19B ALA* 3.9 17.5 - - + -
43B LEU* 4.0 31.2 - - + -
70B TYR* 4.1 10.1 - - + -
71B GLU 3.4 14.1 - - - +
72B LEU* 4.1 12.1 - - + -
115B TYR 4.3 0.2 - - - -
116B GLU* 1.3 74.1 - - - +
118B THR* 1.3 63.2 + - - +
119B PHE* 3.8 33.4 - - + -
149B ASP* 3.3 3.3 - - - +
150B TYR* 2.7 48.7 + - + +
152B PHE* 4.1 15.5 - - + -
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Residues in contact with THR 118 (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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70B TYR* 3.1 7.4 - - - +
71B GLU* 2.8 47.9 + - - -
116B GLU* 5.2 3.1 - - - +
117B LEU* 1.3 76.6 + - - +
119B PHE* 1.3 75.2 + - - +
120B TYR* 3.7 32.0 + - + +
147B LYS* 3.8 15.0 - - + -
148B VAL 3.2 11.4 - - - +
149B ASP* 2.5 24.8 + - - +
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Residues in contact with PHE 119 (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 ILE* 4.2 9.2 - - + -
18B ALA 4.3 2.5 - - - -
19B ALA* 3.8 13.9 - - + -
43B LEU* 4.4 5.4 - - + -
44B GLU 4.5 2.2 - - - -
45B ALA* 3.5 30.7 - - + -
68B ILE* 4.3 4.3 - - + -
69B ALA 3.3 6.1 - - - +
70B TYR* 3.9 11.7 - - + -
85B LEU* 3.7 20.0 - - + -
117B LEU* 3.8 30.9 - - + -
118B THR* 1.3 79.6 - - - +
120B TYR* 1.3 60.1 + - - +
121B ILE* 4.1 14.3 - - + +
146B PHE 3.8 0.2 - - - +
147B LYS* 3.1 8.5 - - - +
148B VAL* 2.9 43.0 + - + +
150B TYR* 3.7 31.6 - + - -
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Residues in contact with TYR 120 (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 THR 3.7 0.9 - - - +
68B ILE* 3.3 4.0 - - - -
69B ALA* 2.9 56.2 + - + +
70B TYR 4.7 0.2 - - - -
71B GLU* 3.5 30.3 + - + -
82B ARG* 3.7 23.3 + - - -
118B THR* 3.7 27.6 + - + +
119B PHE* 1.3 71.9 - - - +
121B ILE* 1.3 60.2 + - - +
122B SER* 5.5 0.4 - - - -
146B PHE 3.4 5.6 - - - +
147B LYS* 4.0 24.5 - - + +
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Residues in contact with ILE 121 (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 MET* 5.2 0.4 - - + -
17B ILE* 3.9 17.7 - - + -
47B ILE* 4.1 15.9 - - + -
66B LEU* 4.2 17.9 - - + -
67B THR 3.3 6.5 - - - +
68B ILE* 4.1 11.2 - - + -
119B PHE* 4.1 24.0 - - + -
120B TYR* 1.3 78.0 - - - +
122B SER* 1.3 73.4 + - - +
143B PHE* 4.0 8.9 - - + -
145B PRO* 3.3 5.4 - - - +
146B PHE* 2.9 74.1 + - + +
148B VAL* 4.4 2.0 - - + -
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Residues in contact with SER 122 (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 LEU* 3.6 10.4 - - - +
67B THR* 2.9 34.2 + - - +
120B TYR 5.5 0.5 - - - -
121B ILE* 1.3 75.9 + - - +
123B ASN* 1.3 65.7 + - - +
126B LYS* 3.7 32.6 - - - +
143B PHE* 3.7 5.4 - - - -
145B PRO* 3.9 23.4 - - - +
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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