Contacts of the strand formed by residues 113 - 122 (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 LEU 113 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E VAL* 3.9 24.7 - - + -
113E LEU* 4.3 22.0 - - + -
137E HIS* 4.2 10.5 - - + +
150E COA 3.1 39.7 + - + +
84G VAL* 4.6 2.0 - - + -
108G LYS 4.3 0.3 - - - +
109G GLN* 3.8 0.7 - - - -
110G GLY* 2.9 26.7 + - - +
112G THR* 1.3 91.7 - - - +
114G ALA* 1.3 59.4 + - - +
115G PHE* 4.1 18.4 - - + -
135G THR* 4.1 13.7 - - + -
136G LYS 3.3 13.5 - - - +
137G HIS* 4.1 8.1 - - + +
138G LEU* 4.2 3.8 - - - +
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Residues in contact with ALA 114 (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* 3.5 38.6 - - + -
108G LYS 3.5 8.1 - - - +
109G GLN* 4.1 4.3 - - + -
113G LEU* 1.3 75.7 - - - +
115G PHE* 1.3 64.0 + - - +
116G THR* 5.1 1.1 - - - -
134G HIS 4.0 0.5 - - - +
135G THR* 3.3 5.9 - - - +
136G LYS* 2.8 33.9 + - + +
138G LEU* 4.0 19.0 - - + +
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Residues in contact with PHE 115 (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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84E VAL* 3.6 26.5 - - + -
150E COA 3.4 27.8 - - - -
89F THR* 3.3 32.3 - - + -
90F TYR 3.7 10.3 - - - -
91F MET* 3.5 29.6 - - + -
106G VAL* 3.6 1.9 - - - +
107G LEU* 2.7 34.4 + - + -
108G LYS* 2.9 33.0 + - + +
113G LEU* 4.1 23.1 - - + -
114G ALA* 1.3 74.4 - - - +
116G THR* 1.3 60.8 + - - +
133G ARG* 6.0 1.1 - - + -
134G HIS 3.7 3.6 - - - -
135G THR* 3.5 14.6 - - + -
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Residues in contact with THR 116 (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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68G SER* 3.2 34.4 + - - +
71G ALA* 5.3 0.2 - - + -
72G LEU* 3.9 35.0 - - + -
105G HIS 3.2 9.4 - - - -
106G VAL* 4.1 12.1 - - + -
107G LEU* 4.1 5.2 - - - +
114G ALA 5.1 0.2 - - - -
115G PHE* 1.3 82.1 - - - +
117G SER* 1.3 60.8 + - - +
118G VAL* 5.3 0.2 - - - -
133G ARG* 3.2 9.6 - - - +
134G HIS* 2.8 51.6 + - - +
136G LYS* 5.9 0.4 - - + -
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Residues in contact with SER 117 (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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131F GLN* 3.9 15.0 + - - -
133F ARG* 5.5 0.2 + - - -
103G THR 3.9 0.7 - - - +
104G ALA* 3.3 0.5 - - - +
105G HIS* 2.9 39.3 + - - +
107G LEU* 4.1 24.2 - - - +
116G THR* 1.3 74.7 - - - +
118G VAL* 1.3 68.8 + - - +
119G ASP* 4.6 2.3 + - - -
131G GLN* 4.4 13.5 - - - +
132G GLY 3.4 12.9 + - - -
133G ARG* 4.6 0.4 - - - -
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Residues in contact with VAL 118 (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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63G LEU 4.9 0.4 - - - +
64G VAL* 3.7 31.9 - - + +
67G ILE* 5.1 0.2 - - + -
68G SER* 3.7 29.4 - - - +
102G ILE* 3.4 32.1 - - + -
103G THR 3.2 9.0 - - - +
104G ALA* 3.8 10.1 - - + -
116G THR* 5.1 0.2 - - - +
117G SER* 1.3 81.6 + - - +
119G ASP* 1.3 66.1 + - - +
120G LEU* 4.0 13.4 - - + +
131G GLN* 3.3 5.2 - - - +
132G GLY 2.8 33.4 + - - +
134G HIS* 5.8 0.4 - - + -
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Residues in contact with ASP 119 (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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101G VAL 3.5 1.7 - - - +
102G ILE* 3.4 2.9 - - - -
103G THR* 2.9 41.7 + - - +
117G SER* 4.6 2.6 + - - -
118G VAL* 1.3 73.6 - - - +
120G LEU* 1.3 62.1 + - - +
121G THR* 4.1 8.4 + - + +
128G LEU* 3.9 19.2 - - + +
130G ALA 3.6 3.6 - - - -
131G GLN* 2.9 33.9 - - - +
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Residues in contact with LEU 120 (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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55G LEU* 4.2 8.5 - - + -
60G THR* 3.8 24.7 - - + +
63G LEU* 4.0 24.7 - - + -
64G VAL* 4.1 18.2 - - + -
100G ILE* 4.1 14.1 - - + -
101G VAL 3.3 4.7 - - - +
102G ILE* 3.9 15.9 - - + -
118G VAL* 4.0 18.8 - - + +
119G ASP* 1.3 76.9 - - - +
121G THR* 1.3 55.8 + - - +
128G LEU* 3.5 5.5 - - - +
129G ILE* 2.8 43.9 + - + -
130G ALA* 2.9 22.9 + - + +
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Residues in contact with THR 121 (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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100G ILE* 3.3 5.0 - - - +
101G VAL* 2.8 54.4 + - - +
103G THR* 5.2 2.3 + - - -
119G ASP* 4.6 9.4 + - + +
120G LEU* 1.3 79.6 - - - +
122G ASN* 1.3 64.4 + - - +
126G GLY* 3.8 21.9 - - - +
127G LYS 3.2 9.0 - - - +
128G LEU* 4.0 16.2 - - + -
129G ILE* 3.6 5.8 - - - -
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Residues in contact with ASN 122 (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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98G GLU* 3.7 40.2 + - - +
99G ASP 3.8 5.5 + - - +
100G ILE* 4.8 0.2 - - - -
121G THR* 1.3 73.4 + - - +
123G LYS* 1.3 59.7 + - - +
124G ALA* 3.0 16.1 + - - +
125G THR* 2.7 49.2 + - - +
126G GLY* 2.8 29.5 + - - -
127G LYS* 2.9 16.0 + - + +
129G ILE* 3.6 14.4 - - + +
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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