Contacts of the strand formed by residues 88 - 93 (chain G) in PDB entry 1U3H
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 GLN 88 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G ALA 3.9 1.8 + - - +
87G PRO* 1.3 76.6 - - - +
89G ALA* 1.3 65.1 + - - +
90G THR* 5.1 8.5 + - - -
108G PHE* 3.5 2.4 - - - +
109G VAL* 3.3 3.9 - - - -
110G ASP* 3.0 38.7 + - + +
111G ASN* 5.4 3.4 - - + -
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Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G PRO 4.3 0.4 - - - -
88G GLN* 1.3 81.1 + - - +
90G THR* 1.3 66.0 + - - +
107G CYS* 4.1 9.9 - - - -
108G PHE 3.3 6.5 - - - +
109G VAL* 4.3 2.5 - - + +
165G VAL* 4.0 26.7 - - + -
174G VAL* 5.8 6.1 - - + +
176G LYS* 3.5 42.5 - - + +
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Residues in contact with THR 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G GLN* 5.1 7.8 + - - -
89G ALA* 1.3 77.3 + - - +
91G VAL* 1.3 66.9 + - - +
92G PHE* 3.9 18.8 - - + -
106G ILE 3.7 1.0 - - - +
107G CYS* 3.6 1.0 - - - -
108G PHE* 2.9 51.6 + - + +
176G LYS* 4.2 5.1 - - - +
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G THR* 1.3 80.9 - - - +
92G PHE* 1.3 66.4 + - - +
105G LEU* 3.4 22.0 - - + -
106G ILE 3.3 7.0 - - - +
107G CYS* 4.0 6.3 - - + -
121G TRP* 4.5 4.0 - - + -
161G TYR 6.4 0.2 - - - -
162G ASP* 6.5 0.2 - - - -
163G CYS* 3.5 33.4 - - + +
176G LYS* 3.9 24.6 - - + +
177G HIS 4.5 3.0 - - - +
178G TRP* 3.4 42.3 - - + -
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Residues in contact with PHE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G THR* 3.9 18.8 - - + -
91G VAL* 1.3 79.8 - - - +
93G PRO* 1.3 72.9 - - + +
105G LEU* 3.7 5.4 - - - -
106G ILE* 2.8 66.6 + - + +
108G PHE* 3.8 28.5 - + + -
148G LEU* 4.8 0.2 - - + -
178G TRP* 4.5 0.4 - - - +
148H ILE* 3.8 24.7 - - + -
149H ARG 4.3 10.1 - - - -
150H ASN* 3.6 23.8 - - - -
156H GLN* 3.7 16.6 - - - +
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Residues in contact with PRO 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G PHE* 1.3 91.4 - - + +
94G LYS* 1.3 64.2 + - - +
95G SER 3.4 18.7 + - - +
96G PRO* 5.6 0.9 - - + -
97G VAL* 3.8 24.2 - - + +
103G ASN* 4.4 4.3 - - - +
104G THR 3.5 8.3 - - - +
105G LEU* 3.9 6.0 - - + -
153G PHE* 5.0 2.2 - - + -
178G TRP* 3.8 23.3 - - + +
156H GLN* 3.2 18.5 + - - +
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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