Contacts of the strand formed by residues 84 - 92 (chain G) in PDB entry 1F1H
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 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G VAL* 4.1 0.9 - - - -
16G PHE* 3.0 12.5 + - - +
18G ASP* 4.0 17.2 + - - +
76G ILE* 3.6 10.6 - - - +
77G ASP* 3.0 31.5 + - + +
80G PHE* 3.4 26.3 - - + -
82G ASP 2.6 30.5 + - - +
83G SER* 1.3 74.1 + - - +
85G LEU* 1.3 59.1 + - - +
86G ILE 4.1 0.2 - - - -
1489G MPD 2.9 38.6 + - + +
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Residues in contact with LEU 85 (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 VAL* 4.0 22.0 - - + -
8G MET* 4.1 26.5 - - + -
9G LEU* 3.8 21.5 - - + -
14G VAL* 3.8 16.3 - - + +
16G PHE 2.8 8.8 + - - +
17G VAL* 3.1 10.8 - - + +
18G ASP 2.7 29.0 + - - -
74G ALA* 4.2 8.3 - - + -
75G VAL* 3.6 30.3 - - - +
76G ILE* 3.8 15.0 - - + +
84G THR* 1.3 73.1 + - - +
86G ILE* 1.3 64.0 - - - +
87G ILE* 4.3 7.6 - - + -
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Residues in contact with ILE 86 (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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18G ASP* 3.4 11.9 - - + +
20G ARG* 3.5 60.3 - - + +
73G THR 3.9 2.1 - - - +
74G ALA* 3.3 2.4 - - - -
75G VAL* 2.6 47.3 + - + +
77G ASP* 3.5 30.5 - - + +
85G LEU* 1.3 72.1 - - - +
87G ILE* 1.3 72.4 + - - +
88G ARG* 4.7 9.6 - - - +
202G MET* 3.6 26.0 - - + -
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Residues in contact with ILE 87 (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 VAL* 4.2 26.5 - - + -
17G VAL* 3.9 23.8 - - + -
18G ASP 2.9 9.7 + - - +
19G LEU* 3.5 12.4 - - + -
20G ARG 3.0 20.3 + - - -
38G VAL* 5.7 0.7 - - + -
42G PHE* 4.8 7.9 - - + -
43G PHE* 4.6 9.9 - - + -
69G PRO* 3.9 20.2 - - + -
70G ASP 3.7 17.7 - - - +
71G ALA* 4.7 2.2 - - - +
73G THR* 3.9 2.7 - - - +
74G ALA* 4.2 11.7 - - + +
85G LEU* 3.9 7.8 + - + -
86G ILE* 1.3 82.2 - - - +
88G ARG* 1.3 73.3 + - - +
89G CYS* 3.7 2.6 - - - -
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Residues in contact with ARG 88 (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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20G ARG* 3.3 22.2 + - - +
21G PHE* 5.1 2.9 - - - +
22G THR* 4.9 3.4 + - - -
28G GLU* 2.5 45.4 + - - +
70G ASP* 3.0 26.2 + - - +
73G THR* 2.9 30.1 + - + +
75G VAL* 6.2 0.8 - - - +
86G ILE* 4.7 11.1 - - - +
87G ILE* 1.3 75.0 - - - +
89G CYS* 1.3 63.7 + - - +
105G ARG* 3.8 18.2 - - - +
233G ASP* 3.4 34.7 + - - +
236G GLN* 3.7 14.4 - - - +
237G ILE* 3.8 29.3 - - - +
368G TYR* 3.8 9.7 + - - -
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Residues in contact with CYS 89 (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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19G LEU* 3.8 27.1 - - - -
20G ARG 2.7 15.0 + - - +
21G PHE* 4.0 11.0 - - - +
67G LEU* 3.6 32.3 - - + -
68G MET 3.3 9.9 - - - +
69G PRO* 3.8 18.6 - - - -
70G ASP 4.4 0.2 - - - +
87G ILE 3.7 11.9 - - - -
88G ARG* 1.3 80.6 - - - +
90G ASP* 1.3 64.1 + - - +
103G ASP* 5.6 0.3 - - - +
105G ARG* 3.8 17.8 - - - +
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Residues in contact with ASP 90 (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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66G VAL 3.4 1.9 - - - +
67G LEU* 3.7 2.6 - - - -
68G MET* 2.8 45.1 + - + +
70G ASP* 4.3 4.7 - - - +
89G CYS* 1.3 73.7 - - - +
91G ILE* 1.3 63.7 + - - +
92G LEU* 3.9 18.4 - - + -
103G ASP* 3.7 7.2 - - - +
105G ARG* 3.0 39.8 + - - +
106G SER* 4.4 4.4 + - - +
109G LYS* 3.1 30.4 + - - +
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Residues in contact with ILE 91 (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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21G PHE* 3.9 23.3 - - + -
49G PHE* 4.0 16.4 - - + -
57G TRP* 3.7 23.8 - - + -
65G MET* 3.7 31.6 - - + -
66G VAL 3.4 2.5 - - - +
67G LEU* 3.6 30.3 - - + -
90G ASP* 1.3 72.8 - - - +
92G LEU* 1.3 62.5 + - - +
99G GLY* 3.7 3.3 - - - -
100G TYR* 3.0 32.0 + - + +
103G ASP* 2.8 33.2 + - + +
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Residues in contact with LEU 92 (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 MET* 3.4 7.5 - - - +
66G VAL* 2.9 40.0 + - + +
68G MET* 3.3 50.0 - - + -
90G ASP* 4.1 15.7 - - + +
91G ILE* 1.3 77.9 - - - +
93G GLU* 1.3 61.4 + - - +
97G LEU* 3.8 30.1 - - + +
98G GLN 4.1 4.9 - - - +
99G GLY* 3.5 25.4 - - - +
100G TYR 4.4 0.9 - - - -
106G SER* 4.6 2.2 - - - +
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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