Contacts of the helix formed by residues 91 - 101 (chain A) in PDB entry 1R9F
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LYS* 4.0 25.2 + - + +
87A LEU 5.7 0.9 - - - +
88A GLY* 5.2 4.7 - - - +
90A TRP* 1.3 87.6 - - - +
92A GLY* 1.3 65.2 + - - +
93A ASP* 3.5 9.3 + - - +
94A SER* 2.9 27.2 + - - -
95A VAL* 3.0 24.8 + - - +
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Residues in contact with GLY 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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90A TRP* 4.4 2.6 - - - -
91A THR* 1.3 74.4 - - - +
93A ASP* 1.3 59.2 + - - +
95A VAL* 3.9 1.4 - - - +
96A ASN* 3.0 30.8 + - - +
134A CYS* 4.3 25.7 - - - -
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Residues in contact with ASP 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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91A THR* 3.1 8.1 + - - +
92A GLY* 1.3 76.2 - - - +
94A SER* 1.3 64.0 + - - +
96A ASN* 3.4 5.7 + - - +
97A TYR* 3.0 26.2 + - - +
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Residues in contact with SER 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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28A SER 4.4 2.6 - - - +
29A PRO* 2.6 30.7 + - - +
30A PHE 5.6 0.2 - - - -
31A LYS* 4.0 17.5 - - - -
90A TRP* 3.5 1.7 - - - +
91A THR* 2.9 36.2 + - - -
93A ASP* 1.3 76.7 - - - +
95A VAL* 1.3 61.1 + - - +
97A TYR* 3.6 6.3 + - - +
98A ALA* 3.2 23.6 + - - +
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Residues in contact with VAL 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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29A PRO* 3.9 14.1 - - + -
63A TRP* 3.5 39.0 - - + +
65A PHE* 3.9 19.8 - - + -
90A TRP* 3.6 15.5 - - + -
91A THR 3.0 20.4 + - - +
92A GLY 3.9 3.1 - - - +
94A SER* 1.3 76.2 - - - +
96A ASN* 1.3 60.2 + - - +
98A ALA* 3.3 1.2 + - - +
99A ALA* 2.8 28.6 + - - +
130A LEU* 4.1 7.2 - - + -
134A CYS* 3.6 20.9 - - - -
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Residues in contact with ASN 96 (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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92A GLY 3.0 19.6 + - - +
93A ASP* 3.8 5.7 + - - +
95A VAL* 1.3 77.0 - - - +
97A TYR* 1.3 59.4 + - - +
100A SER* 2.9 34.5 + - - -
103A PHE* 4.4 11.3 - - - -
130A LEU* 4.0 22.8 - - + +
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Residues in contact with TYR 97 (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* 3.5 35.5 + - + +
93A ASP 3.0 17.0 + - - +
94A SER* 4.0 6.7 - - - +
96A ASN* 1.3 79.7 - - - +
98A ALA* 1.3 62.0 + - - +
100A SER* 3.0 20.4 + - - -
101A ARG* 3.9 5.7 + - - +
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Residues in contact with ALA 98 (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* 3.4 30.9 - - + +
28A SER 3.8 2.7 - - - +
29A PRO* 3.5 29.4 - - + -
65A PHE* 4.1 4.0 - - + -
70A PHE* 5.2 0.2 - - + -
94A SER 3.2 15.8 + - - +
95A VAL 3.8 0.4 - - - +
97A TYR* 1.3 80.3 - - - +
99A ALA* 1.3 62.2 + - - +
101A ARG* 3.5 9.6 - - - +
102A PHE* 3.1 23.7 - - - -
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Residues in contact with ALA 99 (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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65A PHE* 3.4 37.8 - - + -
95A VAL 2.8 21.8 + - - +
96A ASN 4.0 0.2 - - - +
98A ALA* 1.3 69.4 - - - +
100A SER* 1.3 65.6 + - - +
101A ARG 3.1 2.7 - - - -
102A PHE* 2.9 17.5 + - - +
103A PHE* 3.4 18.9 - - + -
108A ILE* 4.7 0.7 - - - +
110A CYS* 5.1 0.2 - - - -
130A LEU* 3.7 20.9 - - + -
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Residues in contact with SER 100 (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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96A ASN* 2.9 24.0 + - - -
97A TYR* 3.0 24.6 + - - -
99A ALA* 1.3 73.2 - - - +
101A ARG* 1.3 62.6 + - - +
102A PHE 3.0 1.3 + - - -
103A PHE* 3.1 39.8 + - - +
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Residues in contact with ARG 101 (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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26A MSE 6.4 1.1 - - + -
27A THR* 6.0 8.7 - - - +
97A TYR 3.9 4.0 + - - +
98A ALA* 3.5 16.3 + - - +
99A ALA 3.0 0.6 + - - -
100A SER* 1.3 81.2 + - - +
102A PHE* 1.3 74.8 + - + +
103A PHE 3.5 2.7 + - - +
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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