Contacts of the strand formed by residues 62 - 75 (chain B) in PDB entry 2IZW
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 ILE 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A HIS* 4.0 15.0 - - + +
58B GLN 5.1 0.2 + - - -
59B TYR* 5.9 1.9 - - - -
60B GLY* 3.8 11.8 + - - +
61B ASP* 1.3 84.6 - - + +
63B THR* 1.3 64.7 + - - +
64B PRO* 3.6 10.3 - - + +
112B ARG* 3.8 12.8 - - - +
181B TRP* 3.4 33.9 - - + -
224B GLU* 3.3 38.8 - - + +
225B LEU 3.4 4.3 - - - +
226B THR* 4.4 1.8 - - - +
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Residues in contact with THR 63 (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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60B GLY* 3.9 10.2 + - - -
61B ASP 4.2 0.4 - - - -
62B ILE* 1.3 75.9 - - - +
64B PRO* 1.3 75.6 - - + +
65B ALA 3.7 0.3 + - - -
104B GLN* 4.8 7.2 - - - +
108B TYR* 3.2 35.4 + - + +
223B VAL 3.6 0.7 - - - +
224B GLU* 3.4 0.5 - - - -
225B LEU* 2.8 49.2 + - + +
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Residues in contact with PRO 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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62B ILE* 3.6 11.4 - - + +
63B THR* 1.3 94.8 - - + +
65B ALA* 1.3 59.3 + - - +
66B LYS* 3.8 2.7 + - + -
104B GLN* 5.5 0.2 - - - +
222B LEU* 4.3 21.3 - - + -
223B VAL 3.5 5.4 - - - +
224B GLU* 4.4 9.4 - - + +
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Residues in contact with ALA 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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64B PRO* 1.3 73.1 - - - +
66B LYS* 1.3 61.0 + - - +
100B TRP* 4.0 8.3 - - + -
101B LEU* 3.9 24.5 - - + -
104B GLN* 4.0 18.2 - - - +
221B TYR* 3.8 7.8 - - - -
222B LEU* 3.2 3.7 - - - -
223B VAL* 2.7 37.0 + - + +
225B LEU* 4.0 15.5 - - + -
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.8 2.6 + - + -
65B ALA* 1.3 72.2 - - - +
67B ASN* 1.3 69.8 + - - +
100B TRP* 4.2 7.1 - - - -
115B TYR* 3.5 19.3 - - + +
220B GLU* 6.5 0.2 - - - -
221B TYR 3.5 10.1 - - - +
222B LEU* 3.2 25.1 - - + -
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Residues in contact with ASN 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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65B ALA 4.0 1.4 + - - -
66B LYS* 1.3 79.9 - - - +
68B SER* 1.3 88.3 + - - +
100B TRP* 3.2 54.7 - - + +
220B GLU* 3.8 2.5 - - - +
221B TYR* 2.8 43.0 + - - +
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Residues in contact with SER 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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67B ASN* 1.3 99.4 + - - +
69B GLY* 1.3 60.4 + - - +
100B TRP* 5.7 1.6 - - - +
219B ALA 2.9 17.5 - - - -
220B GLU* 3.6 16.2 - - - -
221B TYR* 3.8 9.9 + - - -
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Residues in contact with GLY 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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68B SER* 1.3 78.4 + - - +
70B SER* 1.3 64.2 + - - -
71B LEU 3.4 0.9 + - - -
98B LEU* 6.3 2.5 - - - -
218B MET* 3.7 8.5 - - - -
219B ALA* 2.9 32.4 + - - +
221B TYR* 4.6 1.0 - - - -
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Residues in contact with SER 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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69B GLY* 1.3 70.6 - - - -
71B LEU* 1.3 64.3 + - - +
72B VAL 3.9 5.7 + - - -
97B GLU* 3.2 14.8 - - - +
99B PRO* 5.4 1.7 - - - +
216B ARG* 2.9 36.8 + - - +
218B MET* 3.3 26.6 - - - +
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Residues in contact with LEU 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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69B GLY 3.4 2.6 + - - -
70B SER* 1.3 74.7 - - - +
72B VAL* 1.3 62.6 + - + +
88B VAL* 3.9 33.2 - - + -
90B PHE* 5.1 4.7 - - + -
97B GLU* 2.9 33.5 - - + +
98B LEU* 3.4 35.4 - - + -
118B PHE* 4.0 25.6 - - + -
201B ILE* 4.1 13.0 - - + -
217B ILE* 2.7 33.1 + - + +
219B ALA* 4.0 15.5 - - + -
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Residues in contact with VAL 72 (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 SER* 4.3 5.2 - - - -
71B LEU* 1.3 87.5 - - + +
73B ARG* 1.3 61.9 + - - +
74B VAL* 3.8 22.4 - - + -
88B VAL* 3.3 31.2 - - + -
97B GLU* 3.5 13.9 - - + +
203B TRP* 4.3 12.6 - - + +
216B ARG* 3.0 8.7 - - - +
217B ILE* 3.0 45.1 + - + -
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Residues in contact with ARG 73 (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 VAL* 1.3 75.4 - - - +
74B VAL* 1.3 62.9 + - - +
75B THR* 3.5 12.0 + - + +
203B TRP* 5.6 2.1 - - - -
213B THR* 3.6 31.9 - - + +
215B GLY 3.6 4.3 - - - +
216B ARG* 4.0 30.3 - - + +
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Residues in contact with VAL 74 (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 VAL* 3.8 21.7 + - + +
73B ARG* 1.3 73.2 - - - +
75B THR* 1.3 57.3 + - - +
84B VAL* 5.6 1.1 - - + -
120B TRP* 3.8 30.1 - - + -
132B VAL* 5.9 0.7 - - + -
203B TRP* 3.6 42.6 - - + -
205B ALA* 4.0 20.6 - - + -
213B THR* 3.6 0.8 - - - -
214B LEU* 2.7 38.1 + - + +
215B GLY 2.8 12.4 + - - +
217B ILE* 4.4 5.6 - - + -
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Residues in contact with THR 75 (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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73B ARG* 3.9 13.2 - - + +
74B VAL* 1.3 79.1 - - - +
76B SER* 1.3 71.4 + - - +
84B VAL* 4.0 19.6 - - - +
203B TRP* 5.6 0.8 - - - -
211B SER* 4.0 4.3 + - - -
212B THR 3.3 12.9 + - - -
213B THR* 3.3 24.7 - - - +
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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