Contacts of the strand formed by residues 99 - 108 (chain G) in PDB entry 3STJ
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 GLU 99 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G ARG* 5.9 4.0 + - - -
91G SER* 5.8 6.1 - - - -
92G ILE 3.3 7.0 - - - +
93G GLN* 3.3 28.6 - - + +
97G GLY 3.5 4.8 + - - +
98G ARG* 1.3 75.0 - - - +
100G PHE* 1.3 69.9 + - - +
250H SER* 5.5 1.9 - - - -
251H ALA* 3.6 26.4 + - + +
252H ASP* 3.9 19.9 - - - +
255H LYS* 2.9 33.9 + - - +
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Residues in contact with PHE 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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91G SER* 3.3 6.8 - - - -
92G ILE* 2.8 38.4 + - + +
94G LEU* 3.7 35.2 - - + -
98G ARG* 3.5 40.4 - - + -
99G GLU* 1.3 78.8 - - - +
101G ASP* 1.3 63.4 + - - +
118G ILE* 3.5 33.4 - - + -
119G GLN 3.8 4.9 - - - +
120G ASN 3.4 22.7 - - - -
121G PRO* 4.1 1.6 - - + -
122G SER* 4.0 17.7 - - - -
124G LEU* 4.0 6.7 - - + -
255H LYS* 5.3 0.2 - - - +
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Residues in contact with ASP 101 (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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89G LYS* 5.5 5.9 - - - +
90G ILE 3.3 18.7 + - - +
91G SER* 5.1 4.6 - - - -
100G PHE* 1.3 77.2 - - - +
102G ALA* 1.3 62.4 + - - +
118G ILE* 3.5 4.7 - - - -
119G GLN* 2.8 44.4 + - + -
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Residues in contact with ALA 102 (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 ILE* 2.9 37.8 + - + +
92G ILE* 3.5 31.6 - - + -
101G ASP* 1.3 78.6 - - - +
103G LYS* 1.3 65.9 + - - +
116G LEU* 4.4 8.5 - - + -
117G GLN 3.3 14.4 - - - +
118G ILE* 4.5 2.2 - - - +
119G GLN* 4.4 1.8 - - - -
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Residues in contact with LYS 103 (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 ILE* 5.0 0.9 - - - -
102G ALA* 1.3 77.5 - - - +
104G LEU* 1.3 66.3 + - - +
105G ILE* 3.4 7.1 + - + +
116G LEU* 3.3 5.6 - - - -
117G GLN* 2.9 31.6 + - - +
119G GLN* 3.5 38.9 + - + +
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Residues in contact with LEU 104 (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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84G ILE* 4.0 26.0 - - + +
90G ILE* 4.5 12.5 - - + +
103G LYS* 1.3 72.9 - - - +
105G ILE* 1.3 62.6 + - - +
106G GLY* 3.5 30.3 - - - +
107G SER* 4.4 11.9 - - - +
114G ALA* 4.2 4.5 - - + -
115G LEU 3.5 9.2 - - - +
116G LEU* 3.8 19.4 - - + +
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Residues in contact with ILE 105 (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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76G TYR* 4.3 12.3 - - + -
103G LYS* 3.4 6.5 + - + +
104G LEU* 1.3 77.3 - - - +
106G GLY* 1.3 58.9 + - - +
115G LEU* 2.8 30.6 + - + +
116G LEU 4.1 2.0 - - - -
117G GLN* 3.5 48.9 - - + +
231G LEU 3.4 24.5 - - - +
232G ILE* 4.6 3.8 - - - +
235G GLY* 3.8 14.8 - - - +
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Residues in contact with GLY 106 (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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104G LEU* 3.5 11.3 - - - +
105G ILE* 1.3 81.8 - - - +
107G SER* 1.3 61.8 + - - -
115G LEU* 2.8 27.4 + - - +
231G LEU* 3.6 20.7 - - - +
235G GLY 3.9 7.6 - - - -
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Residues in contact with SER 107 (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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81G ASN* 3.3 24.1 + - - -
84G ILE* 5.1 0.4 - - - -
104G LEU* 4.4 14.2 - - - +
106G GLY* 1.3 75.7 - - - -
108G ASP* 1.3 60.4 + - - +
109G ASP* 4.2 8.9 + - - +
113G ILE 3.3 10.5 - - - -
114G ALA* 4.1 8.3 - - - +
231G LEU* 3.6 14.2 - - - +
235G GLY 5.0 0.4 + - - -
236G GLU* 5.4 1.9 - - - -
237G ILE* 5.0 4.9 + - - +
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Residues in contact with ASP 108 (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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81G ASN* 3.9 3.9 - - - +
107G SER* 1.3 73.1 - - - +
109G ASP* 1.3 58.9 + - - +
110G GLN* 3.2 11.1 + - - +
111G SER* 2.6 29.0 + - - +
112G ASP* 2.9 26.2 + - - -
113G ILE* 2.7 21.5 + - + +
227G LEU* 3.7 4.1 - - + +
231G LEU* 5.6 0.2 - - + -
237G ILE* 3.9 23.3 - - + +
239G ARG* 2.9 44.3 + - - -
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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