Contacts of the strand formed by residues 99 - 109 (chain G) in PDB entry 3F5O
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 ASP 99 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41G GLU* 6.1 1.8 - - + -
42G MET 3.5 4.3 - - - +
43G LYS* 3.4 31.0 + - - +
97G GLY 3.7 3.6 + - - +
98G GLU* 1.3 73.0 - - - +
100G ILE* 1.3 63.1 + - - +
122G ASN* 3.8 7.5 + - - +
123G LYS* 2.9 47.2 + - + +
124G ALA 4.6 0.7 + - - +
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Residues in contact with ILE 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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41G GLU* 3.2 8.5 - - - +
42G MET* 2.8 62.2 + - + +
44G VAL* 4.1 9.9 - - + -
55G LEU* 3.8 24.7 - - + -
63G LEU* 4.1 6.7 - - + -
94G ALA* 3.9 13.0 - - + -
98G GLU* 4.2 4.3 - - + +
99G ASP* 1.3 78.6 - - - +
101G VAL* 1.3 64.7 + - - +
102G ILE* 4.1 20.0 - - + -
120G LEU* 4.1 8.3 - - + -
121G THR 3.3 7.6 - - - +
122G ASN* 4.8 0.4 - - - -
123G LYS 4.2 0.2 - - - +
129G ILE* 3.4 26.9 - - + -
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Residues in contact with VAL 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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39G ILE* 3.6 28.3 - - + -
40G CYS 3.4 5.2 - - - +
41G GLU* 3.8 18.6 - - + +
100G ILE* 1.3 77.4 - - - +
102G ILE* 1.3 64.5 + - - +
103G THR* 3.8 10.5 - - - +
119G ASP 3.5 1.6 - - - +
120G LEU* 3.3 4.5 - - - -
121G THR* 2.8 45.7 + - - +
123G LYS* 3.7 31.4 - - + -
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Residues in contact with ILE 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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28G ILE* 5.2 0.7 - - + -
38G VAL 3.7 1.9 - - - +
39G ILE* 3.4 3.1 - - - -
40G CYS* 2.8 55.4 + - + +
41G GLU 4.3 10.5 - - - +
42G MET* 4.3 2.2 - - + +
63G LEU* 4.0 27.1 - - + +
67G ILE* 3.8 27.5 - - + +
100G ILE* 4.1 22.4 - - + -
101G VAL* 1.3 75.3 - - - +
103G THR* 1.3 59.5 + - - +
104G ALA 4.1 0.2 - - - -
118G VAL* 3.4 28.7 - - + -
119G ASP 3.4 3.1 - - - +
120G LEU* 3.9 22.7 - - + -
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Residues in contact with THR 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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37G LYS* 3.8 18.4 - - - +
38G VAL 3.6 2.9 - - - +
39G ILE* 3.9 14.7 - - + +
101G VAL* 3.8 17.0 - - - +
102G ILE* 1.3 75.3 - - - +
104G ALA* 1.3 60.3 + - - +
105G HIS* 3.7 28.8 + - + -
117G SER 3.9 0.5 - - - +
118G VAL* 3.2 5.4 - - - -
119G ASP* 2.9 43.3 + - - +
121G THR* 5.2 2.3 + - - -
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Residues in contact with ALA 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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37G LYS* 3.3 9.7 - - - +
38G VAL 2.8 31.9 + - - +
67G ILE* 3.4 42.0 - - + +
68G SER* 3.8 5.2 - - - -
71G ALA* 4.1 6.0 - - + +
102G ILE 4.1 0.4 - - - -
103G THR* 1.3 73.4 - - - +
105G HIS* 1.3 60.8 + - - +
117G SER 3.3 5.2 - - - -
118G VAL* 3.8 15.0 - - + -
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Residues in contact with HIS 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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36G GLY 3.3 5.2 - - - -
37G LYS* 3.2 39.6 + - + +
71G ALA* 4.8 0.4 - - - -
103G THR* 3.7 26.7 + - + +
104G ALA* 1.3 74.0 - - - +
106G VAL* 1.3 67.8 + - - +
107G LEU* 3.5 11.2 + - + +
116G THR* 3.2 6.0 - - - -
117G SER* 2.9 39.7 + - - +
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Residues in contact with VAL 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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36G GLY* 2.8 26.5 + - - +
71G ALA* 3.6 36.6 - - + +
72G LEU* 3.8 17.0 - - + -
75G THR* 4.2 6.1 - - + -
105G HIS* 1.3 75.4 - - - +
107G LEU* 1.3 62.2 + - - +
108G LYS 4.0 7.6 - - - +
109G GLN* 3.9 28.3 - - + -
115G PHE 3.7 9.9 - - - +
116G THR* 4.1 5.2 - - + -
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Residues in contact with LEU 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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91F MET* 3.8 26.2 - - - -
127F LYS* 5.6 3.8 + - - -
128F LEU* 4.0 26.1 - - + +
131F GLN* 3.8 27.8 - - - +
105G HIS* 3.5 8.5 + - + +
106G VAL* 1.3 75.6 - - - +
108G LYS* 1.3 59.5 + - - +
115G PHE* 2.7 16.1 + - + +
116G THR 4.1 9.6 - - - +
117G SER* 4.1 27.4 - - - +
133G ARG* 4.1 11.0 - - - -
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Residues in contact with LYS 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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150E COA 3.2 31.3 + - - -
91F MET* 3.3 45.8 - - + +
92F SER* 5.0 6.7 - - - -
128F LEU* 5.7 2.2 - - + +
106G VAL* 3.6 3.3 - - - +
107G LEU* 1.3 81.4 - - - +
109G GLN* 1.3 89.0 + - - +
110G GLY* 3.5 4.6 - - - +
114G ALA* 3.5 2.3 - - - +
115G PHE* 2.9 44.8 + - + +
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Residues in contact with GLN 109 (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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72G LEU* 4.2 9.3 - - - +
75G THR* 3.2 39.4 + - - +
77G ARG* 4.3 19.6 - - - +
79G ALA* 5.1 3.3 + - - +
106G VAL* 3.9 17.7 - - + +
108G LYS* 1.3 91.1 + - - +
110G GLY* 1.3 58.3 + - - +
113G LEU 3.9 2.0 - - - -
114G ALA* 4.1 9.2 - - + -
138G LEU* 3.5 23.4 - - - +
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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