Contacts of the helix formed by residues 87 - 95 (chain A) in PDB entry 1FBN
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.7 0.8 - - - +
37A TYR* 3.8 46.6 - - + +
56A LYS* 3.5 34.5 + - + +
57A SER* 4.0 9.0 - - - -
84A SER* 3.8 3.1 + - - -
85A ALA* 3.7 7.7 - - - +
86A GLY* 1.3 74.3 - - - +
88A THR* 1.3 64.7 + - - +
90A SER* 2.7 23.7 + - - -
91A HIS* 3.4 11.2 + - - +
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Residues in contact with THR 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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52A TRP* 4.7 4.3 - - + +
56A LYS 4.7 0.7 + - - -
57A SER* 2.8 35.8 + - - +
58A LYS 4.3 3.3 + - - -
59A LEU* 4.1 19.5 - - + -
80A TYR* 3.4 30.9 + - + +
84A SER* 4.4 0.8 + - - -
87A THR* 1.3 75.9 - - - +
89A PRO* 1.4 66.8 - - - +
91A HIS* 3.1 4.5 + - - +
92A VAL* 3.0 31.6 + - + +
148A TYR* 4.3 8.2 + - + -
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Residues in contact with PRO 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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80A TYR* 3.5 35.0 - - + +
84A SER* 3.2 26.2 - - - +
86A GLY 3.6 5.2 - - - +
87A THR 3.6 2.7 - - - -
88A THR* 1.4 94.3 - - - +
90A SER* 1.3 60.6 + - - +
92A VAL* 3.9 5.8 - - + +
93A ALA* 3.0 24.6 + - - +
101A VAL* 5.3 5.9 - - + +
103A ALA* 5.7 2.5 - - + -
114A LEU* 4.2 21.1 - - + -
118A CYS* 4.2 4.0 - - - -
124A ILE* 3.7 12.8 - - + +
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Residues in contact with SER 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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36A VAL* 3.8 23.9 - - - +
50A ARG* 3.0 28.2 + - - -
86A GLY 2.9 17.2 + - - -
87A THR* 2.7 20.4 + - - -
89A PRO* 1.3 77.1 - - - +
91A HIS* 1.3 60.6 + - - +
93A ALA* 3.4 1.4 + - - +
94A ASP* 3.2 16.1 + - - -
118A CYS* 4.1 4.9 - - - -
121A ARG* 3.2 29.5 + - - +
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Residues in contact with HIS 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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27A THR* 2.8 31.5 - - + +
37A TYR* 2.9 41.7 - + - -
50A ARG* 3.5 29.1 + - - +
51A ILE 4.0 0.8 + - - -
52A TRP* 3.3 59.3 + + + -
87A THR 3.4 16.6 + - - -
88A THR 3.1 6.5 + - - +
90A SER* 1.3 78.4 + - - +
92A VAL* 1.3 65.1 + - - +
94A ASP* 3.2 3.6 + - - +
95A ILE* 3.1 29.4 + - - +
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Residues in contact with VAL 92 (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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52A TRP* 5.2 0.9 - - + -
59A LEU* 4.0 18.8 - - + -
72A ILE* 4.2 17.5 - - + -
78A ILE* 3.6 30.5 - - + -
80A TYR* 4.8 4.7 - - + -
88A THR* 3.0 36.7 + - + +
89A PRO* 3.9 8.3 - - + +
91A HIS* 1.3 75.2 - - - +
93A ALA* 1.3 56.8 + - - +
95A ILE* 3.3 10.3 + - + +
96A ALA* 2.9 28.4 + - - +
101A VAL* 3.9 16.8 - - + -
148A TYR* 5.8 0.9 - - + -
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Residues in contact with ALA 93 (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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30A ILE* 3.6 7.6 - - + +
89A PRO 3.0 18.4 + - - +
90A SER 3.5 6.1 - - - +
91A HIS 3.2 0.2 - - - -
92A VAL* 1.3 74.7 - - - +
94A ASP* 1.3 63.5 + - - +
96A ALA 3.5 7.7 - - - -
97A ASP* 3.5 1.6 + - - -
101A VAL* 4.3 5.8 - - + +
121A ARG* 3.9 9.0 - - - -
123A ASN* 3.0 41.9 + - - +
124A ILE* 3.7 20.4 - - + -
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Residues in contact with ASP 94 (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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12A ASN* 3.2 13.3 - - - +
27A THR* 2.9 27.2 + - - +
28A LYS 3.4 23.0 - - - +
29A SER* 3.6 5.6 - - - -
30A ILE* 3.1 18.2 + - - +
50A ARG* 3.0 22.9 + - - -
90A SER 3.2 9.4 + - - -
91A HIS 3.2 9.3 + - - +
93A ALA* 1.3 79.5 - - - +
95A ILE* 1.3 61.8 + - - +
97A ASP* 3.6 10.9 - - - +
121A ARG* 2.9 24.2 + - - -
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Residues in contact with ILE 95 (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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11A GLU 3.5 23.8 - - - +
12A ASN* 3.0 29.2 - - + +
13A ILE* 3.9 13.9 - - + -
27A THR* 3.8 12.8 - - + -
52A TRP* 3.8 32.1 - - + -
70A MSE 4.1 9.0 - - + -
72A ILE* 3.7 27.6 - - + +
73A LYS 4.3 3.1 - - - +
74A ARG* 3.3 10.9 - - - +
91A HIS 3.1 15.5 + - - +
92A VAL* 3.5 12.3 - - + +
94A ASP* 1.3 75.9 - - - +
96A ALA* 1.3 59.4 + - - +
97A ASP* 3.0 8.7 + - - +
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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