Contacts of the strand formed by residues 128 - 137 (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 128 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F LEU* 3.9 35.2 - - + +
108F LYS* 5.8 1.6 - - + +
91G MET* 3.6 40.5 - - + +
92G SER* 2.8 25.6 + - - -
119G ASP* 3.9 24.7 - - + +
120G LEU 3.5 16.4 - - - +
121G THR* 4.0 7.9 - - + -
126G GLY 3.6 2.8 + - - -
127G LYS* 1.3 77.9 + - - +
129G ILE* 1.3 56.1 + - - +
130G ALA 3.5 16.6 - - - +
131G GLN* 4.7 4.7 - - + +
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Residues in contact with ILE 129 (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* 4.9 4.5 - - + -
60G THR* 5.4 1.8 - - - +
90G TYR* 3.8 2.7 - - + -
91G MET* 2.8 26.8 + - - -
92G SER* 3.2 31.0 + - - +
93G PRO 4.8 2.5 - - - +
94G ALA* 3.7 23.1 - - + +
98G GLU* 5.4 1.1 - - - +
100G ILE* 3.4 34.3 - - + -
120G LEU* 2.8 25.7 + - + +
121G THR 3.6 4.9 - - - +
122G ASN* 3.6 30.3 - - + +
127G LYS 4.1 0.9 - - - +
128G LEU* 1.3 73.9 - - - +
130G ALA* 1.3 66.3 + - + +
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Residues in contact with ALA 130 (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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60G THR* 4.0 27.1 - - + -
88G ILE* 4.2 6.1 - - + -
89G THR 3.1 16.8 - - - +
90G TYR* 4.3 7.0 - - + -
91G MET* 4.0 6.1 - - - -
120G LEU* 2.9 33.5 + - + +
128G LEU* 3.5 6.6 - - - +
129G ILE* 1.3 86.6 - - + +
131G GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 131 (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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105F HIS* 5.8 0.5 - - - -
107F LEU* 3.7 23.1 - - - +
117F SER* 3.9 13.1 + - - -
131F GLN* 5.3 4.4 - - - +
133F ARG* 2.8 43.9 - - - +
64G VAL* 5.4 0.4 - - - -
88G ILE* 3.5 4.4 - - - -
89G THR* 2.9 30.7 + - - -
91G MET* 3.6 13.2 - - + +
117G SER* 4.4 8.9 + - - +
118G VAL 3.3 5.2 - - - +
119G ASP* 2.9 27.4 - - - +
128G LEU* 4.7 4.0 - - + +
130G ALA* 1.3 76.3 - - - +
132G GLY* 1.3 65.0 + - - +
133G ARG* 5.4 0.8 - - - +
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Residues in contact with GLY 132 (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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133F ARG* 3.3 8.9 + - - -
64G VAL* 4.4 19.8 - - - +
87G ASN 3.0 14.6 - - - -
88G ILE* 4.1 2.5 - - - -
117G SER* 3.4 9.0 + - - -
118G VAL 2.8 33.3 + - - -
131G GLN* 1.3 74.3 - - - +
133G ARG* 1.3 59.2 + - - +
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Residues in contact with ARG 133 (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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85E ASP* 5.8 0.2 - - - +
87F ASN* 2.8 29.9 + - - +
88F ILE 4.2 0.8 - - - -
89F THR* 2.8 41.5 + - + +
117F SER* 5.5 0.2 + - - -
131F GLN* 2.8 44.8 + - - +
132F GLY* 3.3 9.3 + - - +
133F ARG* 3.3 33.4 - - - +
64G VAL* 4.8 0.2 - - - +
85G ASP 4.6 0.2 - - - -
86G MET* 3.3 5.4 - - - +
87G ASN* 3.0 51.1 + - - +
107G LEU* 4.1 9.6 - - + -
115G PHE* 6.0 0.7 - - + -
116G THR 3.2 21.5 - - - +
117G SER* 4.4 1.1 - - - +
131G GLN* 5.4 1.0 - - - +
132G GLY* 1.3 74.1 - - - +
134G HIS* 1.3 61.7 + - - +
135G THR* 5.8 0.9 - - - +
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Residues in contact with HIS 134 (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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64G VAL* 4.5 5.8 - - + -
65G ASP* 3.2 32.3 + - - -
68G SER* 2.8 25.9 + - - +
83G SER* 2.7 28.5 + - - -
85G ASP 3.4 11.9 - - - -
86G MET* 4.1 19.4 - - + -
114G ALA 4.0 0.5 - - - +
115G PHE* 3.7 0.9 - - - -
116G THR* 2.8 47.1 + - - +
118G VAL* 5.8 0.7 - - + -
133G ARG* 1.3 78.8 - - - +
135G THR* 1.3 69.6 + - - +
136G LYS* 3.5 26.2 - - + +
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Residues in contact with THR 135 (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* 4.0 9.6 - - + -
85E ASP* 2.7 33.6 + - - +
89F THR* 3.9 2.8 + - - +
84G VAL* 2.8 35.3 + - + -
85G ASP 2.8 18.6 + - - +
113G LEU* 4.1 16.4 - - + -
114G ALA 3.3 11.7 - - - +
115G PHE* 3.5 28.3 - - + +
133G ARG* 5.7 1.2 - - - +
134G HIS* 1.3 74.8 + - - +
136G LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 136 (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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65G ASP* 4.6 0.8 + - - -
69G THR* 2.8 27.4 + - - +
72G LEU* 3.7 21.3 - - + -
80G PRO 2.8 28.1 + - - +
81G GLY* 3.1 8.2 + - - -
82G VAL 3.2 7.6 - - - +
83G SER* 3.6 20.4 + - - +
84G VAL* 4.0 3.6 - - - +
113G LEU* 3.3 6.8 - - - +
114G ALA* 2.8 34.9 + - - +
116G THR* 5.6 0.7 - - + +
134G HIS* 3.5 35.9 - - + +
135G THR* 1.3 77.7 - - - +
137G HIS* 1.3 61.0 + - - +
138G LEU* 3.9 2.6 + - + -
149G UOC 3.0 21.1 + - - +
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Residues in contact with HIS 137 (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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112E THR* 3.6 13.7 + - + -
113E LEU* 4.1 8.3 - - + +
81G GLY* 3.1 2.4 - - - -
82G VAL* 2.8 39.2 + - + +
84G VAL* 3.5 20.8 - - + +
112G THR* 3.3 25.1 + - + -
113G LEU* 4.1 2.8 - - + +
136G LYS* 1.3 72.5 - - - +
138G LEU* 1.3 77.0 + - - +
139G GLY 4.0 1.5 + - - -
150G COA 2.7 80.5 + - + -
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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