Contacts of the strand formed by residues 16 - 22 (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 PHE 16 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 2.9 9.3 - - - +
15G LYS* 1.3 94.4 - - + +
17G VAL* 1.3 64.9 + - - +
32G THR* 3.6 22.9 - - + -
33G ILE 3.5 2.9 - - - -
34G PRO* 3.9 20.4 - - + -
35G ALA 3.8 1.1 - - - +
82G ASP* 4.0 8.1 - - + -
83G SER 3.1 4.2 + - - -
84G THR* 3.0 3.2 - - - -
85G LEU 2.8 22.9 + - - -
1489G MPD 2.9 32.5 - - + -
193H SER* 3.6 32.5 - - - -
196H CYS* 4.0 18.4 - - + -
197H LEU* 3.5 33.7 - - + -
209H HIS* 4.3 4.5 - + - -
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Residues in contact with VAL 17 (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* 6.3 0.2 - - + -
9G LEU* 4.1 20.0 - - + -
16G PHE* 1.3 80.1 - - - +
18G ASP* 1.3 61.1 + - - +
19G LEU* 3.5 27.8 + - + +
32G THR* 3.4 4.2 - - - +
33G ILE* 2.7 47.8 + - + +
35G ALA* 4.4 6.1 - - - -
38G VAL* 3.7 26.5 - - + -
42G PHE* 5.1 0.7 - - + -
85G LEU* 3.1 15.9 - - + +
87G ILE* 3.9 18.4 - - + -
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Residues in contact with ASP 18 (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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17G VAL* 1.3 69.9 - - - +
19G LEU* 1.3 66.3 + - - +
20G ARG* 2.7 35.8 + - - +
30G HIS* 2.8 28.0 - - - +
31G VAL 3.5 4.4 - - - +
32G THR* 2.6 27.1 + - + +
80G PHE* 4.1 8.5 - - + -
84G THR* 4.0 15.3 + - - +
85G LEU 2.7 11.4 + - - +
86G ILE* 3.4 13.6 - - + +
87G ILE 2.9 25.2 + - - -
189H GLN* 4.2 0.2 - - - +
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Residues in contact with LEU 19 (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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17G VAL* 3.5 26.4 + - + -
18G ASP* 1.3 71.3 - - - +
20G ARG* 1.3 61.1 + - - +
21G PHE* 4.7 2.7 - - - -
30G HIS* 3.1 6.2 - - - -
31G VAL* 2.8 55.7 + - + +
33G ILE* 4.4 25.1 - - + -
42G PHE* 4.1 29.4 - - + -
47G LYS* 5.2 7.2 - - + -
67G LEU* 4.5 13.7 - - + -
87G ILE* 3.5 14.4 - - + +
89G CYS* 3.8 19.3 - - - -
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Residues in contact with ARG 20 (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* 2.7 27.8 + - - +
19G LEU* 1.3 77.7 - - - +
21G PHE* 1.3 62.9 + - - +
28G GLU* 3.1 32.0 + - - +
29G GLN 3.2 11.7 - - - +
30G HIS* 3.8 0.9 - - + -
77G ASP* 2.9 23.8 + - - -
80G PHE* 3.4 10.5 - - - -
86G ILE* 3.5 43.5 - - + +
87G ILE 3.0 8.4 + - - +
88G ARG* 3.3 13.8 - - - +
89G CYS* 2.7 33.4 + - - +
202G MET* 5.1 0.8 - - - +
240G TYR* 3.4 37.6 + - - +
182H VAL* 4.0 10.3 - - - +
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Residues in contact with PHE 21 (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 4.7 2.7 - - - -
20G ARG* 1.3 79.5 - - - +
22G THR* 1.3 64.1 + - - +
23G ASP* 5.3 0.4 - - - -
28G GLU* 3.3 5.3 - - - -
29G GLN* 2.5 68.2 + - + +
30G HIS* 4.7 2.0 - - - -
31G VAL* 5.2 0.9 - - + -
49G PHE* 4.3 16.6 - + - -
54G ILE* 4.5 9.0 - - + -
57G TRP* 3.7 35.4 - + - -
67G LEU* 3.7 27.8 - - + -
88G ARG* 5.2 5.8 - - - +
89G CYS 4.0 14.8 - - - +
91G ILE* 3.9 13.7 - - + -
103G ASP* 6.0 0.9 - - - +
180H PHE* 4.1 22.7 - + - -
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Residues in contact with THR 22 (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* 1.3 81.8 - - - +
23G ASP* 1.3 76.8 + - - +
26G GLY* 3.5 27.8 - - - -
27G LYS 3.6 3.1 - - - -
28G GLU* 4.3 1.4 - - - +
57G TRP* 3.6 9.2 - - - -
88G ARG* 4.9 1.9 + - - -
103G ASP* 4.7 2.3 + - - +
104G PRO* 3.6 19.0 - - + +
105G ARG* 5.9 2.8 - - - +
236G GLN* 2.8 25.7 + - - +
366G ASN* 4.1 6.7 - - - +
368G TYR* 3.4 31.7 + - + -
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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