Contacts of the strand formed by residues 92 - 98 (chain G) in PDB entry 3IYD
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 CYS 92 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G LYS* 3.9 3.2 - - - +
23G TYR* 3.4 27.4 + - - +
29G LEU* 5.1 4.0 - - - -
42G ILE* 5.0 4.0 - - + -
44G LYS 3.2 15.5 - - - +
45G GLY 4.2 0.4 - - - -
46G SER 3.4 33.0 - - - +
47G VAL* 4.8 5.8 - - - -
88G ALA* 4.2 15.5 - - - -
90G THR 3.0 10.5 + - - -
91G ALA* 1.3 76.1 - - - +
93G GLU* 1.3 60.8 + - - +
94G VAL* 3.9 18.2 + - + +
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Residues in contact with GLU 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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20G ILE* 3.3 37.8 - - + +
22G LYS* 3.3 41.2 + - + +
42G ILE* 4.0 0.3 - - - +
43G VAL* 3.1 39.0 + - + +
44G LYS* 2.9 42.6 + - + +
92G CYS* 1.3 71.1 - - - +
94G VAL* 1.3 67.3 + - - +
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Residues in contact with VAL 94 (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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19G HIS 4.2 0.5 - - - +
20G ILE* 4.6 0.7 - - - -
21G HIS* 3.9 19.6 + - - +
22G LYS* 4.2 7.7 + - - +
23G TYR* 4.3 14.5 - - + -
29G LEU* 4.0 20.2 - - + -
40G TYR* 3.5 21.8 - - + -
41G TYR 3.3 23.6 - - - +
42G ILE* 4.4 16.2 - - + -
70G ILE* 4.4 4.7 - - + -
92G CYS* 3.9 17.5 + - - -
93G GLU* 1.3 83.4 - - - +
95G ALA* 1.3 75.4 + - - +
96G GLU* 4.5 4.0 - - - +
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Residues in contact with ALA 95 (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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14G PHE* 5.8 0.2 - - + -
15G LEU* 4.6 10.3 - - + -
18G CYS* 3.6 32.1 - - + -
19G HIS 4.0 7.4 - - - +
20G ILE* 5.1 3.8 - - + +
39G LEU 4.4 0.4 - - - -
40G TYR* 3.5 12.6 - - - -
41G TYR* 3.0 20.9 + - + +
43G VAL* 5.1 5.1 - - + +
94G VAL* 1.3 87.5 - - - +
96G GLU* 1.3 66.3 + - - +
97G ILE* 4.3 2.7 - - + -
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Residues in contact with GLU 96 (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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18G CYS 4.1 1.4 - - - -
19G HIS* 3.4 55.7 + - + +
21G HIS* 3.4 19.8 + - - +
23G TYR* 2.9 23.1 + - - -
38G THR* 4.0 13.2 - - + +
39G LEU 3.5 3.8 - - - -
40G TYR* 3.8 16.6 - - + -
94G VAL 4.5 3.1 - - - +
95G ALA* 1.3 83.5 - - - +
97G ILE* 1.3 66.6 + - - +
98G SER 4.3 0.4 - - - -
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Residues in contact with ILE 97 (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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14G PHE* 4.0 30.1 - - + +
17G HIS 3.9 17.5 - - - +
18G CYS* 3.6 28.9 - - + -
38G THR* 4.3 2.4 - - - +
39G LEU* 2.8 45.0 + - + +
95G ALA* 5.3 1.8 - - + -
96G GLU* 1.3 81.1 - - - +
98G SER* 1.3 74.6 + - - +
101G LYS* 4.7 7.4 - - + -
102G PHE* 4.3 22.9 - - + +
105G LEU* 4.6 14.1 - - + -
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Residues in contact with SER 98 (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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37G GLU 4.0 17.5 - - - -
38G THR* 4.5 3.4 - - - +
96G GLU 4.3 0.4 - - - -
97G ILE* 1.3 77.6 - - - +
99G TYR* 1.3 65.3 + - - +
100G LYS* 4.1 7.1 - - - +
101G LYS* 3.3 40.5 + - - +
102G PHE* 3.0 19.1 + - - +
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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