Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 1XTP
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.2 11.2 - - + -
71A MSE 3.0 33.0 - - + +
73A HIS* 1.3 78.4 - - + +
75A HIS* 1.3 65.7 + - - +
76A ASP 3.4 0.9 - - - -
77A VAL* 3.1 11.8 - - - +
78A ASP* 3.0 22.7 + - - +
166A TRP* 4.6 9.6 - - + -
241A TRP* 3.5 32.1 - - + -
242A PRO* 4.0 24.7 - - + -
245A LEU* 4.1 10.3 - - + -
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Residues in contact with HIS 75 (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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64A VAL* 4.8 7.6 - - + +
68A LEU* 3.9 11.7 - - + -
72A ASP 3.2 16.2 + - - +
73A HIS 3.2 1.0 - - - -
74A VAL* 1.3 78.4 - - - +
76A ASP* 1.3 83.0 + - - +
78A ASP* 3.1 7.6 + - - +
79A ILE* 2.9 45.0 + - + +
106A ARG* 3.0 48.6 + - + +
110A ASN* 3.5 26.0 + - - +
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Residues in contact with ASP 76 (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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73A HIS 4.6 5.2 + - - +
74A VAL 3.4 0.6 - - - -
75A HIS* 1.3 96.0 - - - +
77A VAL* 1.3 63.6 + - - +
79A ILE* 3.4 4.3 + - - +
80A GLU* 3.1 25.5 + - - +
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Residues in contact with VAL 77 (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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73A HIS 4.9 2.4 + - - +
74A VAL* 3.1 28.3 - - + +
76A ASP* 1.3 75.0 - - - +
78A ASP* 1.3 65.8 + - - +
80A GLU* 3.4 5.0 + - - +
81A GLY 3.0 20.1 + - - -
238A GLN* 3.3 23.8 + - + +
239A GLU 3.6 11.4 - - - +
240A GLU* 3.7 30.3 - - + +
241A TRP* 3.9 17.0 - - + -
242A PRO* 5.3 2.0 - - + -
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Residues in contact with ASP 78 (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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74A VAL 3.0 20.2 + - - +
75A HIS* 3.4 5.4 - - - +
77A VAL* 1.3 78.7 - - - +
79A ILE* 1.3 66.6 + - - +
82A SER* 3.1 10.3 + - - -
106A ARG* 2.9 32.8 + - - +
165A GLN* 2.8 25.0 + - - +
166A TRP* 4.1 9.2 - - + -
196A LYS* 2.7 50.8 + - - +
238A GLN* 4.1 4.7 - - - -
241A TRP* 4.4 9.2 - - + -
248A LEU* 3.9 3.6 - - - +
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Residues in contact with ILE 79 (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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75A HIS* 2.9 45.0 + - + +
76A ASP* 3.9 4.7 - - - +
78A ASP* 1.3 78.0 - - - +
80A GLU* 1.3 59.2 + - - +
82A SER* 3.4 5.3 + - - +
83A ARG* 3.0 28.9 + - + +
106A ARG* 3.6 17.9 - - - +
107A ILE* 4.4 19.3 - - + -
110A ASN* 3.7 33.0 - - + +
111A LEU* 4.1 18.6 - - + +
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Residues in contact with GLU 80 (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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76A ASP 3.1 17.9 + - - +
77A VAL* 3.9 5.4 - - + +
79A ILE* 1.3 79.3 - - - +
81A GLY* 1.3 56.7 + - - +
83A ARG* 2.9 42.6 + - - +
84A ASN* 3.0 44.6 + - - +
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Residues in contact with GLY 81 (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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77A VAL 3.0 11.7 + - - -
80A GLU* 1.3 77.2 - - - +
82A SER* 1.3 55.1 + - - +
84A ASN* 3.6 6.0 + - - +
85A PHE* 3.0 29.8 + - - +
238A GLN* 3.4 24.4 - - - +
239A GLU* 6.2 1.6 - - - -
250A MSE 3.6 12.6 - - - +
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Residues in contact with SER 82 (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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78A ASP* 3.1 11.9 + - - -
79A ILE* 3.7 3.7 - - - +
80A GLU 3.3 0.2 - - - -
81A GLY* 1.3 72.4 - - - +
83A ARG* 1.3 60.6 + - - +
85A PHE* 3.3 0.7 + - - +
86A ILE* 2.8 37.5 + - - +
107A ILE* 6.2 0.7 - - - -
111A LEU* 3.5 21.5 - - - -
165A GLN* 4.2 4.7 + - - -
194A PHE* 3.3 29.0 - - - -
196A LYS* 2.8 26.6 + - - +
250A MSE 4.0 2.0 - - - -
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Residues in contact with ARG 83 (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 ILE* 3.0 20.0 + - + +
80A GLU* 2.9 39.7 + - - +
82A SER* 1.3 77.1 - - - +
84A ASN* 1.3 74.9 + - - +
86A ILE* 3.9 3.4 - - - +
87A ALA* 2.9 38.3 + - + +
111A LEU* 3.6 26.8 - - + +
114A LYS* 6.1 4.9 - - - -
115A LEU* 4.8 13.6 - - + +
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Residues in contact with ASN 84 (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 GLU* 3.0 38.7 + - - +
81A GLY* 4.0 5.6 - - - +
83A ARG* 1.3 99.5 + - - +
85A PHE* 1.3 67.0 + - - +
87A ALA* 3.5 7.1 + - - +
88A SER* 3.3 20.1 + - - -
239A GLU* 5.7 2.6 + - - -
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Residues in contact with PHE 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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81A GLY 3.0 19.4 + - - +
82A SER* 3.6 2.5 - - - +
84A ASN* 1.3 77.6 - - - +
86A ILE* 1.3 64.4 + - - +
88A SER* 2.5 25.8 + - - -
89A LEU* 3.6 10.9 - - + +
194A PHE* 3.3 32.1 - + - -
234A LYS* 3.7 33.2 - - + -
236A ALA* 4.1 31.6 - - + -
250A MSE 3.6 22.0 - - + -
251A TYR 4.0 3.4 - - - -
252A ALA* 3.6 42.2 - - + -
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Residues in contact with ILE 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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82A SER* 2.8 28.6 + - - +
83A ARG* 4.0 2.9 - - - +
85A PHE* 1.3 71.8 - - - +
87A ALA* 1.3 63.5 + - - +
89A LEU* 3.1 27.5 + - + +
92A HIS* 3.2 24.3 + - + +
111A LEU* 3.9 23.6 - - + -
112A LEU* 5.0 1.6 - - + -
115A LEU* 4.5 18.6 - - + -
116A TYR* 3.7 21.1 - - + +
161A LEU* 3.8 24.5 - - + -
163A VAL* 5.8 0.2 - - + -
194A PHE* 4.1 24.0 - - + -
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Residues in contact with ALA 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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83A ARG* 2.9 28.5 + - + +
84A ASN* 3.6 9.6 - - - +
85A PHE 3.3 0.2 - - - -
86A ILE* 1.3 76.2 - - - +
88A SER* 1.3 60.4 + - - +
89A LEU 3.4 1.6 + - - +
92A HIS* 3.5 18.4 - - - -
115A LEU* 6.5 1.6 - - + -
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Residues in contact with SER 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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84A ASN 3.3 8.2 + - - -
85A PHE* 2.5 24.8 + - - -
87A ALA* 1.3 78.7 - - - +
89A LEU* 1.3 62.0 + - - +
90A PRO* 3.4 10.7 - - - +
234A LYS* 3.6 23.0 - - - +
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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