Contacts of the strand formed by residues 156 - 162 (chain G) in PDB entry 5FLM
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 156 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G CYS* 4.4 3.6 - - + -
44G PHE* 3.2 26.7 - - - -
103G PRO 5.3 1.4 - - - +
105G SER* 5.7 0.7 + - - -
151G ARG 3.9 0.2 - - - +
152G VAL* 3.1 1.5 - - - +
153G ASP* 2.3 44.9 + - - +
154G LYS 2.8 7.1 + - - +
155G ASN* 1.3 76.6 - - - +
157G ILE* 1.3 65.7 + - - +
158G PHE* 3.9 8.5 + - - +
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Residues in contact with ILE 157 (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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38G CYS* 3.9 7.6 - - - -
40G GLY* 3.5 28.3 - - - +
43G GLY* 3.6 26.2 - - - -
44G PHE* 3.6 21.2 - - + -
78G ARG* 5.5 2.7 - - + -
79G PRO* 4.7 9.9 - - + -
104G MET* 3.4 30.9 - - - +
105G SER* 4.8 0.9 + - - -
150G THR* 4.5 10.5 - - - -
151G ARG 3.1 20.4 - - - +
152G VAL* 3.6 22.0 - - + +
155G ASN 3.9 0.2 + - - -
156G ASP* 1.3 78.3 + - - +
158G PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 158 (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 MET* 4.0 1.6 - - - -
105G SER* 3.8 23.1 - - - +
107G PHE* 6.4 2.0 - - + -
151G ARG* 2.3 88.8 + - + +
153G ASP* 3.4 33.2 - - + -
156G ASP* 4.1 11.0 - - - +
157G ILE* 1.3 70.7 - - - +
159G ALA* 1.3 61.6 + - - +
160G ILE* 5.7 7.6 - - + -
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Residues in contact with ALA 159 (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 MET* 3.7 28.2 - - + -
105G SER 3.4 6.9 + - - +
106G CYS* 3.4 5.6 - - - -
107G PHE* 3.0 24.5 + - - +
147G ILE* 3.6 17.7 - - + -
149G GLY 3.1 16.2 - - - +
150G THR* 4.3 6.3 - - + -
158G PHE* 1.3 77.0 - - - +
160G ILE* 1.3 67.7 + - - +
161G GLY 4.2 0.2 - - - -
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Residues in contact with ILE 160 (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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106G CYS* 4.0 1.8 - - - -
107G PHE* 3.2 31.6 - - + +
108G ILE* 5.0 1.1 - - - -
109G SER* 5.4 1.1 - - - +
112G SER* 5.0 6.5 - - - +
147G ILE* 3.1 4.5 - - - -
148G VAL* 2.3 48.1 + - + -
149G GLY* 2.9 18.7 + - - +
151G ARG* 6.5 0.7 - - + -
158G PHE* 5.7 8.1 - - + -
159G ALA* 1.3 79.2 - - - +
161G GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 161 (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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106G CYS* 3.3 6.3 - - - -
107G PHE 3.1 7.5 + - - -
108G ILE* 3.2 26.5 - - - +
112G SER* 4.1 3.1 - - - -
145G LEU* 3.9 16.2 - - - -
146G LYS 3.2 10.8 - - - -
148G VAL* 4.0 2.0 - - - -
160G ILE* 1.3 86.2 - - - +
162G SER* 1.3 63.2 + - - -
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Residues in contact with SER 162 (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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108G ILE* 3.9 9.8 - - - +
112G SER* 2.8 34.0 + - - -
145G LEU* 4.0 2.8 - - - -
146G LYS* 3.0 27.6 + - - +
148G VAL* 3.7 17.3 - - - -
161G GLY* 1.3 76.0 - - - -
163G LEU* 1.3 62.3 + - - +
164G MET* 3.1 21.0 + - - +
168G LEU* 3.7 7.1 - - - +
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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