Contacts of the strand formed by residues 98 - 104 (chain G) in PDB entry 6S1M
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 98 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91G ARG 4.7 0.2 - - - +
92G ALA* 4.4 12.5 - - - +
93G GLU 4.5 0.3 + - - -
96G ALA* 3.0 29.8 + - + +
97G ASP* 1.3 81.0 - - - +
99G LEU* 1.3 69.8 + - - +
100G ALA 4.3 0.2 + - - -
115G GLU* 4.1 19.4 + - - +
116G MET 3.4 14.3 + - - -
117G LYS* 4.7 4.0 - - - -
118G LEU* 3.5 7.8 - - - +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G PHE* 4.7 0.7 - - + -
28G TRP* 6.5 1.3 - - + -
68G MET* 4.0 22.2 - - + -
70G VAL* 5.1 4.7 - - + -
75G MET* 5.0 8.3 - - + -
90G LEU* 4.5 20.2 - - + -
91G ARG 3.4 29.8 - - - +
92G ALA* 3.8 11.2 - - + -
98G THR* 1.3 75.5 + - - +
100G ALA* 1.3 69.1 + - - +
101G LEU* 4.3 11.2 - - + -
114G TYR 3.8 0.2 - - - +
115G GLU* 3.4 2.6 - - - -
116G MET* 2.7 57.7 + - + +
118G LEU* 3.7 17.3 - - + +
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Residues in contact with ALA 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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89G THR 3.1 6.4 - - - +
90G LEU* 3.6 3.1 - - - -
91G ARG* 2.9 57.9 + - + +
99G LEU* 1.3 76.6 - - - +
101G LEU* 1.3 63.7 + - - +
102G VAL* 4.0 0.9 - - + -
113G ASP* 4.6 3.8 - - - +
114G TYR 3.2 3.6 - - - -
115G GLU* 3.6 26.2 - - - +
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Residues in contact with LEU 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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75G MET* 4.7 9.0 - - + -
78G ILE* 4.0 15.5 - - + -
79G LEU* 3.6 36.8 - - + -
88G ILE* 5.0 0.4 - - + -
89G THR 3.7 3.1 - - - -
90G LEU* 4.3 19.5 - - + -
99G LEU* 4.3 9.6 - - + -
100G ALA* 1.3 77.2 - - - +
102G VAL* 1.3 60.2 + - - +
103G PHE* 3.9 20.2 - - + -
112G SER 3.9 0.5 - - - +
113G ASP* 3.5 0.9 - - - -
114G TYR* 2.5 53.7 + - + +
116G MET* 4.3 32.5 - - + -
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Residues in contact with VAL 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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87G ILE 3.4 3.6 - - - +
89G THR* 2.9 45.7 + - - +
91G ARG* 3.7 27.8 - - - +
100G ALA 5.0 2.5 - - - -
101G LEU* 1.3 73.6 - - - +
103G PHE* 1.3 68.8 + - - +
104G GLU* 4.6 11.9 - - + +
111G VAL* 3.7 21.3 - - + -
112G SER 3.2 11.2 - - - +
113G ASP* 3.2 25.1 - - + +
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Residues in contact with PHE 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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78G ILE* 4.0 10.3 - - + -
79G LEU* 4.0 8.7 - - + -
81G CYS 3.6 22.7 - - - -
82G ALA* 3.6 20.0 - - + -
86G ASP* 4.1 17.3 - - + +
87G ILE 3.3 2.7 - - - -
88G ILE* 3.5 37.2 - - + -
101G LEU* 3.9 33.9 - - + -
102G VAL* 1.3 78.3 - - - +
104G GLU* 1.3 62.5 + - - +
105G ALA 4.0 0.6 + - - -
110G LYS 4.1 0.2 - - - +
111G VAL* 3.4 6.2 - - - +
112G SER* 2.7 41.3 + - - +
114G TYR* 3.7 30.3 - + - -
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Residues in contact with GLU 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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5G ARG* 3.4 37.9 + - - -
86G ASP* 3.1 4.3 - - - -
87G ILE* 2.6 51.1 + - + +
89G THR* 4.1 8.5 + - - -
102G VAL* 4.6 9.3 - - + +
103G PHE* 1.3 76.7 - - - +
105G ALA* 1.3 64.1 + - - +
106G PRO 3.7 0.3 - - - -
108G GLN* 2.7 41.0 + - - +
110G LYS 4.1 0.7 - - - -
111G VAL* 4.3 11.2 - - + -
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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