Contacts of the helix formed by residues 93 - 101 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84K LEU 6.1 0.2 - - - +
85K TYR 6.4 0.2 - - - -
86K GLN 3.6 2.5 - - - +
87K LYS* 3.6 23.5 - - + -
91K GLY 3.6 7.6 - - - +
92K VAL* 1.3 90.0 - - + +
94K PHE* 1.3 66.6 + - - +
95K VAL* 3.0 7.2 - - + +
96K ARG* 2.8 49.8 + - + +
97K THR* 3.1 5.9 + - - -
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Residues in contact with PHE 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K ARG* 3.4 29.2 - - + -
60K ARG* 4.1 7.2 - - + -
61K GLN* 3.8 24.5 - - + -
64K PHE* 3.3 33.2 - + + -
79K PHE* 3.8 11.0 - - + -
83K THR* 3.9 8.5 - - + +
86K GLN* 3.1 50.3 + - + +
87K LYS 3.8 11.0 - - - -
88K ASP* 3.7 28.5 - - + -
92K VAL 3.2 2.2 + - - -
93K PRO* 1.3 70.9 - - - +
95K VAL* 1.3 62.8 + - - +
97K THR* 3.3 7.5 + - - -
98K ILE* 3.1 29.4 + - - +
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Residues in contact with VAL 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K PHE* 4.2 12.8 - - + -
84K LEU* 3.2 52.0 - - + +
86K GLN 5.9 0.2 - - - +
93K PRO* 3.0 6.4 - - + -
94K PHE* 1.3 78.2 - - - +
96K ARG* 1.3 64.6 + - - +
98K ILE* 3.4 1.4 + - - +
99K GLN* 2.8 51.2 + - + +
105K VAL* 4.0 14.1 - - + -
141K ASP 3.8 19.1 - - - +
142K GLY* 4.6 0.4 - - - -
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Residues in contact with ARG 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K VAL* 4.1 11.9 - - + +
93K PRO* 2.8 41.0 + - + +
95K VAL* 1.3 79.2 - - - +
97K THR* 1.3 57.7 + - - +
99K GLN* 3.1 16.7 + - - +
100K ASP* 2.8 53.9 + - - +
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Residues in contact with THR 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K PHE* 3.6 24.7 - - + +
65K SER* 5.6 1.1 - - - -
88K ASP* 4.4 7.6 + - - -
92K VAL* 3.7 15.2 + - - +
93K PRO 3.1 8.8 + - - -
94K PHE* 3.5 14.0 - - - -
96K ARG* 1.3 78.4 - - - +
98K ILE* 1.3 68.0 + - + +
100K ASP* 3.0 19.8 + - - +
101K LYS* 3.2 26.6 + - + +
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Residues in contact with ILE 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K PHE* 3.5 45.1 - - + +
77K VAL* 3.9 23.1 - - + -
79K PHE* 4.1 11.9 - - + -
94K PHE 3.1 19.8 + - - +
95K VAL 3.9 2.2 - - - +
97K THR* 1.3 80.3 - - + +
99K GLN* 1.3 62.1 + - - +
101K LYS* 3.2 12.3 + - + +
103K ILE* 3.2 56.0 + - + +
104K VAL 4.2 1.1 - - - +
105K VAL* 3.9 14.4 - - + -
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Residues in contact with GLN 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K VAL* 2.8 36.5 + - - +
96K ARG* 3.3 17.6 - - - +
98K ILE* 1.3 78.0 - - - +
100K ASP* 1.3 60.5 + - - +
102K GLY* 2.8 22.0 + - - -
103K ILE 3.9 6.7 - - - +
105K VAL* 3.7 14.8 - - + -
142K GLY* 3.7 30.9 + - - -
144K ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K LYS* 5.4 1.9 + - - -
96K ARG* 2.8 46.4 + - - +
97K THR* 3.0 10.0 + - - +
99K GLN* 1.3 69.9 - - - +
101K LYS* 1.3 59.0 + - + +
102K GLY 3.0 9.9 + - - -
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Residues in contact with LYS 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K PHE 4.4 3.8 - - - -
66K ALA 3.0 28.7 + - - -
67K ASP* 3.5 10.0 - - - +
68K ASP* 3.4 25.1 + - - +
70K VAL* 4.0 21.1 - - + -
71K LYS* 3.3 39.6 - - + +
97K THR* 3.2 28.2 + - + +
98K ILE* 3.7 10.1 - - + +
99K GLN 3.2 1.2 - - - -
100K ASP* 1.3 75.8 - - + +
102K GLY* 1.3 60.9 + - - +
103K ILE* 3.4 12.5 + - + +
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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