Contacts of the strand formed by residues 97 - 100 (chain G) in PDB entry 5UQ9
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 97 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G PRO* 3.9 21.3 - - + +
69G ARG 3.2 23.6 + - - +
70G ARG* 3.5 29.4 - - + -
71G ILE* 3.2 14.8 + - - +
95G GLY 4.3 0.2 - - - +
96G ASP* 1.3 81.5 - - - +
98G ILE* 1.3 67.4 + - - +
99G ILE* 4.2 4.7 - - + -
122G LEU* 3.2 31.0 - - + +
124G VAL* 5.8 0.2 - - + -
148G GLU 5.0 0.4 - - - +
149G ALA* 3.4 33.9 - - + -
152G HIS* 4.6 8.7 - - + +
153G ILE* 5.0 4.3 - - + -
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ILE* 3.4 7.9 - - + +
73G LEU* 3.7 33.7 - - + -
85G ILE* 4.5 11.9 - - + -
88G LEU* 4.3 20.9 - - + -
89G VAL* 5.8 2.9 - - + -
92G LEU* 3.5 30.3 - - + -
97G ILE* 1.3 77.7 - - - +
99G ILE* 1.3 63.4 + - - +
116G LEU* 6.0 1.3 - - + -
121G ILE* 3.6 25.8 - - + -
122G LEU 3.2 5.5 + - - +
123G PHE* 3.4 24.7 - - + -
124G VAL* 3.1 23.7 + - - +
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Residues in contact with ILE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.7 6.1 - - + -
70G ARG* 5.1 2.5 - - + -
71G ILE 2.6 19.0 + - - +
72G ILE* 3.3 27.5 - - + -
73G LEU* 2.5 37.2 + - - +
97G ILE* 5.0 6.7 - - + -
98G ILE* 1.3 79.5 - - - +
100G ASP* 1.3 58.9 + - - +
101G GLY* 3.9 1.7 + - - +
124G VAL* 3.3 28.3 - - + +
126G SER* 4.3 9.2 - - - -
153G ILE* 3.6 31.2 - - + -
157G PHE* 3.8 27.1 - - + -
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Residues in contact with ASP 100 (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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73G LEU* 3.6 10.7 - - + +
74G LEU* 5.3 0.2 - - - -
76G LYS 5.4 0.9 + - - -
81G VAL* 3.9 30.5 - - + +
98G ILE 4.1 0.6 + - - -
99G ILE* 1.3 71.9 - - - +
101G GLY* 1.3 58.9 + - - +
102G GLY* 3.1 18.3 + - - -
104G SER* 3.0 26.2 + - - -
109G THR* 4.9 0.2 + - - -
112G ARG* 4.2 3.8 + - - -
123G PHE* 3.5 27.3 - - + -
124G VAL 2.8 10.4 + - - +
125G GLY* 4.5 2.2 - - - -
126G SER 2.9 28.4 + - - +
181G HIS* 3.5 9.7 + - + -
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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
------------------------------------------------------------
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