Contacts of the helix formed by residues 84 - 91 (chain A) in PDB entry 2FPM
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 SER 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A THR* 3.1 12.1 - - - -
83A SER* 1.3 80.7 - - - +
85A SER* 1.3 64.2 + - - +
86A GLU* 3.5 3.1 + - - -
87A LEU* 3.0 26.2 + - - +
88A ASP* 3.0 25.7 + - - -
312A ILE 4.2 1.9 + - - -
313A PHE* 3.6 21.5 - - - +
320A ILE* 3.9 17.9 - - - -
321A GLN 4.8 0.7 - - - -
322A ASP* 3.4 8.0 + - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER 4.0 1.0 + - - -
84A SER* 1.3 72.1 - - - +
86A GLU* 1.3 58.8 + - - -
88A ASP* 3.5 6.6 + - - +
89A SER* 3.1 27.7 + - - -
322A ASP* 2.7 30.3 + - - -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER* 3.5 1.2 + - - -
85A SER* 1.3 81.0 - - - +
87A LEU* 1.3 59.6 + - - +
89A SER* 3.2 7.6 + - - -
90A VAL* 2.9 32.6 + - + +
310A GLU 4.2 4.9 - - - +
311A ALA* 3.5 12.8 - - + -
312A ILE* 3.0 55.2 + - - +
322A ASP* 4.1 2.1 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A THR* 3.5 28.0 - - + +
84A SER* 3.0 21.1 + - - +
86A GLU* 1.3 73.1 - - - +
88A ASP* 1.3 67.4 + - - +
90A VAL* 3.2 1.3 + - + +
91A LEU* 2.9 36.9 + - + +
103A PHE* 4.3 17.5 - - + -
114A ILE* 4.9 9.6 - - + -
286A PHE* 3.6 34.8 - - + -
298A ALA* 4.0 18.6 - - + -
311A ALA* 3.4 11.8 - - + +
313A PHE* 4.8 11.0 - - + -
320A ILE* 5.6 2.5 - - + -
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 2.7 29.3 + - - -
82A THR* 2.8 35.7 + - - +
83A SER 4.3 0.5 + - - -
84A SER 3.0 22.0 + - - +
85A SER* 3.7 6.3 - - - +
87A LEU* 1.3 74.8 - - - +
89A SER* 1.3 55.8 + - - +
91A LEU* 3.4 4.7 + - - -
92A GLY 3.3 3.1 + - - -
93A GLY* 2.7 51.8 + - - +
94A GLY* 3.4 1.9 + - - -
129A PHE* 4.2 6.2 - - - -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 3.1 14.4 + - - -
86A GLU* 3.4 11.2 - - - -
87A LEU 3.1 0.2 - - - -
88A ASP* 1.3 74.3 - - - +
90A VAL* 1.3 62.6 + - - +
92A GLY* 2.9 20.6 + - - -
93A GLY* 4.6 2.0 - - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLU 2.9 19.4 + - - +
87A LEU* 3.2 4.5 + - + +
89A SER* 1.3 76.1 - - - +
91A LEU* 1.3 60.6 + - - +
92A GLY 3.1 1.1 + - - -
286A PHE* 3.9 12.8 - - + -
298A ALA 5.2 0.2 - - - +
300A LEU* 3.6 37.1 - - + +
306A LEU* 3.5 15.6 - - - +
307A PRO 5.2 0.7 - - - +
309A ALA* 3.9 26.4 - - + +
310A GLU 3.9 14.8 - - - +
311A ALA* 3.8 19.5 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 5.0 0.3 + - - -
82A THR* 3.6 20.6 - - + -
87A LEU* 2.9 25.9 + - + +
88A ASP 3.7 5.2 - - - +
89A SER 3.1 0.2 - - - -
90A VAL* 1.3 76.4 - - - +
92A GLY* 1.3 60.3 + - - +
94A GLY* 3.5 29.9 - - - +
95A LEU* 3.6 32.5 - - + -
96A GLU* 4.6 7.0 - - - +
101A THR* 5.2 3.1 - - + -
103A PHE* 5.2 0.2 - - + -
284A PHE* 4.4 21.7 - - + -
286A PHE* 3.4 36.6 - - + -
300A LEU* 5.6 0.2 - - - -
305A HIS* 5.5 0.2 + - - -
306A LEU* 3.4 15.5 - - - +
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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