Contacts of the helix formed by residues 93 - 101 (chain D) in PDB entry 1XFB
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 PRO 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D LEU 6.1 0.2 - - - +
85D TYR 6.4 0.2 - - - -
86D GLN 3.6 2.7 - - - +
87D LYS* 3.6 22.6 - - + -
91D GLY 3.6 7.2 - - - +
92D VAL* 1.3 89.7 - - + +
94D PHE* 1.3 67.0 + - - +
95D VAL* 4.2 7.0 - - + +
96D ARG* 2.8 49.8 + - + +
97D THR* 3.1 5.9 + - - -
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 3.4 29.8 - - + -
60D ARG* 4.1 7.4 - - + -
61D GLN* 3.8 24.7 - - + -
64D PHE* 3.3 33.9 - + + -
79D PHE* 3.8 10.5 - - + -
83D THR* 3.9 8.7 - - + +
86D GLN* 3.1 50.0 + - + +
87D LYS 3.8 10.5 - - - -
88D ASP* 3.7 28.7 - - + -
92D VAL 3.2 2.4 + - - -
93D PRO* 1.3 71.3 - - - +
95D VAL* 1.3 63.3 + - + +
97D THR* 3.3 7.7 + - - -
98D ILE* 3.1 30.0 + - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 4.2 12.6 - - + -
84D LEU* 3.2 52.5 - - + +
86D GLN 5.9 0.4 - - - +
93D PRO* 3.0 6.4 - - + -
94D PHE* 1.3 78.4 - - - +
96D ARG* 1.3 63.4 + - - +
98D ILE* 3.4 1.7 + - - +
99D GLN* 2.8 51.2 + - + +
105D VAL* 4.0 14.4 - - + -
141D ASP 3.8 19.7 - - - +
142D GLY* 4.6 0.7 - - - -
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Residues in contact with ARG 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D VAL* 4.1 11.4 - - + +
93D PRO* 2.8 41.0 + - + +
95D VAL* 1.3 78.1 - - - +
97D THR* 1.3 58.5 + - - +
99D GLN* 3.1 16.4 + - - +
100D ASP* 2.8 53.2 + - - +
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Residues in contact with THR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.6 25.6 - - + +
65D SER* 5.6 0.7 - - - -
88D ASP* 4.4 7.8 + - - +
92D VAL* 3.7 15.6 + - - +
93D PRO 3.1 8.3 + - - -
94D PHE* 3.5 13.4 - - - -
96D ARG* 1.3 78.2 - - - +
98D ILE* 1.3 68.0 + - + +
100D ASP* 3.0 19.2 + - - +
101D LYS* 3.2 27.0 + - - +
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.5 44.4 - - + +
77D VAL* 3.9 23.8 - - + -
79D PHE* 4.1 11.7 - - + -
94D PHE 3.1 20.6 + - - +
95D VAL 3.9 2.2 - - - +
97D THR* 1.3 81.4 - - + +
99D GLN* 1.3 63.3 + - - +
101D LYS* 3.2 13.2 + - + +
103D ILE* 3.2 55.9 + - + +
104D VAL 4.2 1.1 - - - +
105D VAL* 3.9 13.7 - - + -
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Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 2.8 37.4 + - - +
96D ARG* 3.3 17.2 - - - +
98D ILE* 1.3 76.8 - - - +
100D ASP* 1.3 60.9 + - - +
102D GLY* 2.8 22.0 + - - -
103D ILE 3.9 7.9 - - - +
105D VAL* 3.7 15.3 - - + -
142D GLY* 3.7 30.7 + - - -
144D ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LYS* 5.4 2.3 + - - -
96D ARG* 2.8 44.6 + - - +
97D THR* 3.0 10.9 + - - +
99D GLN* 1.3 70.1 - - - +
101D LYS* 1.3 58.4 + - + +
102D GLY* 3.0 8.7 + - - -
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Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE 4.4 3.8 - - - -
66D ALA 3.0 29.3 + - - -
67D ASP* 3.5 10.0 - - - +
68D ASP* 3.4 25.1 + - - +
70D VAL* 4.0 21.3 - - + -
71D LYS* 3.3 40.1 - - + +
97D THR* 3.2 28.4 + - + +
98D ILE* 3.7 10.3 - - + +
99D GLN 3.2 1.0 - - - -
100D ASP* 1.3 76.9 - - + +
102D GLY* 1.3 60.6 + - - +
103D ILE* 3.2 12.7 + - + +
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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