Contacts of the strand formed by residues 96 - 104 (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 THR 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B GLU* 3.2 25.5 + - - +
77B ILE 3.0 6.1 - - - -
78B THR* 3.4 28.5 - - + +
94B GLY 3.7 6.1 - - - +
95B ARG* 1.3 85.2 - - - +
97B PHE* 1.3 68.4 + - - +
98B PRO* 4.7 1.0 - - - +
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Residues in contact with PHE 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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76B GLU* 3.1 9.7 - - - +
77B ILE* 2.7 45.9 + - + +
79B ILE* 4.1 22.7 - - + -
90B PHE* 3.5 36.6 - + - -
95B ARG* 3.3 49.1 - - + -
96B THR* 1.3 79.2 - - - +
98B PRO* 1.3 78.0 - - + +
123B PHE* 3.8 41.1 - + + +
131B PRO* 4.5 4.5 - - + -
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Residues in contact with PRO 98 (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 3.8 6.7 - - - +
76B GLU* 4.7 3.1 - - + -
96B THR 4.7 1.1 - - - +
97B PHE* 1.3 90.5 - - + +
99B ALA* 1.3 59.0 + - - +
123B PHE 3.1 9.2 - - - +
124B ALA* 2.9 25.2 + - - -
125B ASP* 4.0 23.6 - - + +
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Residues in contact with ALA 99 (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* 3.3 8.5 - - - +
75B GLY* 2.9 39.6 + - - +
76B GLU* 4.5 0.4 - - - -
77B ILE* 3.6 30.3 - - + -
97B PHE 4.2 0.4 - - - +
98B PRO* 1.3 77.0 - - - +
100B ARG* 1.3 67.7 + - - +
121B ILE* 5.7 1.6 - - + -
122B LYS 3.1 15.7 - - - +
124B ALA 3.7 4.6 - - - -
125B ASP* 4.3 3.6 - - - +
306B VAL* 6.1 0.4 - - + -
308B ILE* 5.7 4.7 - - + -
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Residues in contact with ARG 100 (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 3.5 4.7 - - - +
74B ILE* 4.2 7.2 - - + -
99B ALA* 1.3 81.3 - - - +
101B LEU* 1.3 61.3 + - - +
120B SER 3.8 0.3 - - - +
121B ILE* 3.3 5.4 - - - +
122B LYS* 2.9 36.9 + - + +
124B ALA 3.6 10.0 + - - +
125B ASP* 2.9 29.3 + - - +
126B SER* 3.3 32.8 + - - +
127B ASP* 2.7 28.9 + - - -
308B ILE* 5.3 0.4 - - - -
312B LEU* 4.0 15.5 - - + +
316B VAL* 3.4 20.5 - - - +
320B THR* 2.9 33.1 + - + -
322B PHE* 3.8 4.0 - - + -
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Residues in contact with LEU 101 (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* 3.1 4.8 - - - -
73B GLY 2.9 32.7 + - - +
100B ARG* 1.3 75.8 - - - +
102B ARG* 1.3 71.3 + - - +
103B HIS* 3.5 29.2 - - + +
119B PHE* 3.4 37.9 - - + -
120B SER 3.3 9.9 - - - +
121B ILE* 3.9 7.4 - - + -
258B TYR* 3.8 15.5 - - + +
269B TYR* 3.7 20.0 - - + -
306B VAL* 4.5 0.7 - - + -
308B ILE* 3.7 22.7 - - + -
312B LEU* 4.8 0.6 - - - +
317B LEU* 4.0 4.3 - - - +
322B PHE* 4.5 1.6 - - - -
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Residues in contact with ARG 102 (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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63B ARG* 4.6 0.4 - - - +
64B ARG* 3.3 41.4 - - - +
67B HIS* 2.9 29.9 + - - +
68B THR 3.1 18.2 + - - -
70B GLY* 3.4 19.0 - - - +
71B THR 3.4 9.9 - - - +
101B LEU* 1.3 80.0 - - - +
103B HIS* 1.3 64.1 + - - +
104B ALA* 3.5 10.1 + - - +
118B SER* 4.0 2.8 + - - +
119B PHE* 3.8 3.8 + - - -
120B SER* 2.9 32.2 + - - +
317B LEU* 3.7 29.0 - - + +
318B GLU* 4.6 3.6 + - - +
322B PHE* 3.8 15.5 - - + -
999B HEM 2.8 40.8 + - - +
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Residues in contact with HIS 103 (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* 3.1 3.8 - - - -
71B THR* 2.7 37.2 + - + +
101B LEU* 3.5 17.2 - - + +
102B ARG* 1.3 75.6 - - - +
104B ALA* 1.3 61.5 + - - +
118B SER 2.7 24.9 - - - -
119B PHE* 3.7 16.4 - - - -
187B PHE* 3.5 41.9 + + + +
192B TYR* 3.3 26.7 + + - -
258B TYR* 3.6 11.0 - + - -
269B TYR* 2.6 35.8 - + - -
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Residues in contact with ALA 104 (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* 3.8 12.1 - - + -
69B VAL 3.2 18.4 - - - +
70B GLY* 4.1 0.9 - - - -
102B ARG* 3.5 23.6 - - - +
103B HIS* 1.3 77.5 - - - +
105B ASN* 1.3 66.1 + - - +
106B LEU 3.8 0.2 + - - -
117B ARG* 3.3 5.5 - - - -
118B SER* 2.8 41.5 + - - +
187B PHE* 3.9 8.5 - - - -
999B HEM 4.8 0.2 - - - +
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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