Contacts of the strand formed by residues 28 - 34 (chain G) in PDB entry 1FPY
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 GLU 28 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G ARG* 3.4 22.1 + - + -
21G PHE 3.5 9.2 - - - +
22G THR* 4.3 0.4 - - - +
26G GLY 3.4 4.2 + - - -
27G LYS* 1.3 72.8 - - - +
29G GLN* 1.3 74.8 + - - +
88G ARG* 2.6 37.1 + - - +
236G GLN* 3.5 38.2 - - - +
237G ILE* 5.1 1.9 + - - +
240G TYR* 4.1 10.6 + - - +
181H PRO* 4.0 0.3 - - - +
182H VAL* 3.4 48.6 + - + +
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Residues in contact with GLN 29 (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* 3.0 8.7 - - - +
21G PHE* 2.6 72.1 + - + +
23G ASP* 4.1 14.2 + - + +
27G LYS* 2.6 44.0 + - - +
28G GLU* 1.3 88.4 + - - +
30G HIS* 1.3 62.9 + - - +
54G ILE* 5.0 7.3 - - + +
179H TYR 3.0 25.1 - - - +
180H PHE* 3.0 18.5 - - + +
181H PRO* 3.4 6.8 - - - +
182H VAL* 4.4 1.6 - - - -
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Residues in contact with HIS 30 (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* 2.9 41.1 - - - +
19G LEU 2.9 9.2 - - - +
20G ARG* 3.6 10.1 - - + -
21G PHE* 5.2 0.9 - - - -
29G GLN* 1.3 79.6 - - - +
31G VAL* 1.3 66.1 + - - +
32G THR* 3.9 1.6 - - - -
80G PHE* 5.1 0.2 - + - -
180H PHE* 3.1 32.3 + - - +
181H PRO 3.3 22.3 + - - -
182H VAL* 3.7 9.1 - - + -
183H PRO* 3.5 13.4 - - + +
186H ASP* 3.1 25.6 + - - -
189H GLN* 3.3 26.7 + - + +
192H ARG* 3.8 3.7 + - - -
210H HIS* 4.9 2.5 - - - +
211H HIS* 5.8 2.2 + - + -
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Residues in contact with VAL 31 (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 0.9 - - - +
18G ASP* 3.3 1.6 - - - +
19G LEU* 2.7 68.2 + - + +
21G PHE* 5.5 1.6 - - + -
30G HIS* 1.3 78.8 - - - +
32G THR* 1.3 71.0 + - - +
33G ILE* 3.9 8.9 + - + -
67G LEU* 4.0 17.3 - - + -
180H PHE* 4.1 18.4 - - + -
208H ALA* 5.2 2.7 - - + -
209H HIS 3.8 12.1 - - - +
210H HIS* 3.9 17.7 - - + +
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Residues in contact with THR 32 (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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16G PHE* 3.6 28.7 - - + -
17G VAL 3.3 11.7 - - - +
18G ASP* 2.7 13.6 + - + +
30G HIS* 3.9 0.7 - - - -
31G VAL* 1.3 73.0 - - - +
33G ILE* 1.3 73.9 + - - +
34G PRO* 4.4 0.2 - - - +
84G THR* 5.6 1.6 - - - +
189H GLN* 2.6 31.4 + - - +
192H ARG* 4.4 0.2 + - - -
208H ALA* 3.2 0.9 - - - +
209H HIS* 2.9 63.5 + - - +
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Residues in contact with ILE 33 (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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16G PHE* 3.4 5.4 - - - -
17G VAL* 2.6 45.9 + - + +
19G LEU* 4.6 21.3 - - + -
31G VAL* 4.5 10.3 - - + -
32G THR* 1.3 80.3 - - - +
34G PRO* 1.3 74.4 - - - +
37G GLN* 3.6 14.8 - - + +
38G VAL* 4.0 17.9 - - + -
42G PHE* 5.5 4.0 - - + -
47G LYS* 5.0 16.8 - - + +
207H GLU 3.4 12.8 - - - +
208H ALA* 3.1 27.1 - - + -
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Residues in contact with PRO 34 (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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15G LYS 3.7 8.1 - - - +
16G PHE* 3.9 16.2 - - + -
32G THR 4.4 0.2 - - - +
33G ILE* 1.3 96.4 - - - +
35G ALA* 1.3 66.8 + - - +
36G HIS* 3.5 25.8 - - + +
37G GLN* 2.9 17.4 + - + -
200H GLU* 4.8 3.1 - - - +
206H VAL* 3.1 35.2 - - + +
207H GLU 3.1 22.0 - - - +
208H ALA* 4.0 3.1 - - - +
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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