Contacts of the strand formed by residues 70 - 79 (chain B) in PDB entry 1U5U
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ARG* 4.8 2.2 - - - +
69B VAL* 1.3 77.2 - - - +
71B THR* 1.3 63.0 + - - -
102B ARG* 3.4 15.1 - - - +
103B HIS 3.1 14.1 - - - -
104B ALA* 4.1 0.2 - - - -
255B ARG* 3.6 19.5 + - - +
317B LEU* 3.9 11.3 - - - +
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Residues in contact with THR 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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70B GLY* 1.3 75.0 - - - -
72B GLY* 1.3 61.1 + - - +
102B ARG* 3.4 4.0 - - - +
103B HIS* 2.7 37.9 + - + +
187B PHE* 3.8 26.7 - - + -
255B ARG* 3.2 25.4 + - - +
258B TYR* 3.6 28.4 - - + +
259B VAL* 3.5 18.5 - - - +
317B LEU* 3.5 13.1 - - - +
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Residues in contact with GLY 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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71B THR* 1.3 82.2 + - - +
73B GLY* 1.3 58.2 + - - -
101B LEU* 3.1 14.8 - - - -
102B ARG* 4.3 0.2 - - - -
258B TYR* 4.0 18.7 - - - -
259B VAL* 5.3 2.8 - - - +
262B LEU* 4.2 2.8 - - - +
311B PRO* 3.6 6.6 - - - +
312B LEU* 2.9 24.4 + - - +
317B LEU* 3.8 9.0 - - - +
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Residues in contact with GLY 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 GLY* 1.3 75.0 - - - -
74B ILE* 1.3 65.6 + - - -
75B GLY 4.3 0.2 + - - -
100B ARG* 3.5 2.8 - - - +
101B LEU* 2.9 33.5 + - - +
258B TYR* 4.6 0.6 - - - -
262B LEU* 4.5 0.2 - - - -
308B ILE* 3.8 16.8 - - - +
310B THR 3.0 14.4 - - - -
312B LEU* 3.4 12.2 - - - +
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Residues in contact with ILE 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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73B GLY* 1.3 74.3 - - - +
75B GLY* 1.3 58.2 + - - +
99B ALA 3.3 7.6 - - - +
100B ARG* 4.2 7.6 - - + -
125B ASP* 4.0 30.5 - - - +
308B ILE* 3.7 2.4 - - - +
309B LYS* 3.0 22.7 + - - +
310B THR* 2.8 41.2 + - + +
311B PRO 5.5 0.2 - - - +
312B LEU* 3.4 28.9 - - + -
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Residues in contact with GLY 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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74B ILE* 1.3 77.4 - - - +
76B GLU* 1.3 63.4 + - - +
98B PRO* 3.8 4.5 - - - +
99B ALA* 2.9 30.4 + - - +
307B SER 3.1 14.8 - - - -
308B ILE* 4.1 5.8 - - - +
309B LYS* 4.1 8.7 - - - -
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Residues in contact with GLU 76 (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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75B GLY* 1.3 76.0 - - - +
77B ILE* 1.3 64.5 + - - +
78B THR* 4.1 8.2 + - - +
96B THR* 3.2 31.1 + - - +
97B PHE 3.1 25.2 - - - +
98B PRO* 4.7 1.8 - - + -
99B ALA* 4.4 1.3 - - - +
305B LYS 3.7 1.2 - - - +
306B VAL* 3.7 2.7 - - - +
307B SER* 2.9 35.0 + - - +
308B ILE* 5.1 1.0 - - - +
309B LYS* 3.7 23.8 + - - +
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Residues in contact with ILE 77 (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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76B GLU* 1.3 75.2 - - - +
78B THR* 1.3 62.1 + - - +
79B ILE* 4.6 1.6 - - + -
95B ARG 3.6 1.4 - - - +
96B THR* 3.0 4.5 - - - -
97B PHE* 2.7 46.3 + - + +
99B ALA* 3.6 27.8 - - + -
121B ILE* 4.2 14.1 - - + -
122B LYS 4.2 1.1 - - - +
123B PHE* 3.4 57.4 - - + -
271B LEU* 5.0 0.9 - - + -
304B ALA* 3.9 21.3 - - + -
305B LYS 3.5 4.5 - - - +
306B VAL* 4.3 17.9 - - + -
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Residues in contact with THR 78 (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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76B GLU* 4.4 11.1 + - - +
77B ILE* 1.3 75.7 - - - +
79B ILE* 1.3 73.0 + - - +
80B VAL* 4.5 0.7 - - - -
81B ASN* 5.9 0.9 - - - +
94B GLY* 4.0 7.9 - - - +
95B ARG 3.3 1.8 - - - -
96B THR* 3.4 27.8 - - + +
304B ALA* 3.5 3.1 - - - -
305B LYS* 2.8 47.9 + - - +
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Residues in contact with ILE 79 (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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77B ILE* 4.6 6.3 - - + -
78B THR* 1.3 78.3 - - - +
80B VAL* 1.3 75.7 + - + +
81B ASN* 3.7 0.7 + - - +
83B PRO* 5.3 0.2 - - + -
85B PHE* 4.4 10.5 - - + -
91B PHE* 3.8 44.9 - - + +
92B THR 3.4 28.5 - - - +
93B ALA* 4.1 1.1 - - - -
94B GLY* 3.0 17.8 + - - -
95B ARG* 2.8 22.3 + - + +
97B PHE* 4.1 19.7 - - + -
123B PHE* 4.8 1.6 - - + -
271B LEU* 6.1 0.2 - - + -
303B LEU* 3.4 13.9 - - + +
304B ALA* 3.8 15.3 - - + -
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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