Contacts of the helix formed by residues 87 - 104 (chain P) in PDB entry 2XTJ
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 HIS 87 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P GLU* 3.6 17.7 + - - +
86P THR* 1.3 76.3 - - - +
88P LEU* 1.3 60.8 + - - +
89P SER* 3.2 12.7 + - - +
90P GLN* 2.9 41.6 + - - +
91P SER* 3.0 14.1 + - - -
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Residues in contact with LEU 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P HIS* 1.3 73.6 - - - +
89P SER* 1.3 57.4 + - - +
91P SER* 3.3 5.4 + - - -
92P GLU* 3.1 43.1 + - - +
114P VAL* 3.8 27.1 - - + +
115P PHE 4.3 12.3 - - - +
116P HIS* 4.1 41.5 - - + +
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Residues in contact with SER 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P HIS* 4.1 10.8 + - - +
88P LEU* 1.3 76.1 - - - +
90P GLN* 1.3 68.3 + - - +
92P GLU* 3.5 8.4 + - - +
93P ARG* 3.1 50.2 + - - +
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Residues in contact with GLN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P GLU 4.5 1.1 + - - +
86P THR* 3.5 25.5 - - + +
87P HIS* 2.9 47.9 + - + +
89P SER* 1.3 78.7 + - - +
91P SER* 1.3 58.5 + - - +
93P ARG* 3.5 21.5 + - - +
94P THR* 3.0 32.1 + - - -
139P HIS* 3.9 28.5 + - - +
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Residues in contact with SER 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P LEU* 3.3 26.6 - - - +
86P THR* 4.0 3.3 - - - +
87P HIS 3.0 13.7 + - - -
88P LEU* 3.5 13.8 - - - -
89P SER 3.2 0.2 - - - -
90P GLN* 1.3 75.5 - - - +
92P GLU* 1.3 64.5 + - - +
94P THR* 3.3 4.0 + - - -
95P ALA* 3.0 23.4 + - - +
114P VAL* 4.0 19.1 - - - -
115P PHE 4.8 1.6 + - - -
120P PRO* 4.1 6.2 - - - +
121P GLY 3.9 14.8 + - - -
122P PHE* 4.0 4.3 - - - -
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Residues in contact with GLU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P LEU* 3.1 35.1 + - - +
89P SER* 3.9 7.9 - - - +
91P SER* 1.3 77.1 - - - +
93P ARG* 1.3 56.3 + - - +
95P ALA* 3.3 6.9 + - - +
96P ARG* 2.9 53.6 + - - +
114P VAL* 4.1 23.5 - - + +
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Residues in contact with ARG 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P SER* 3.1 48.2 + - - +
90P GLN* 3.7 28.9 - - - +
91P SER 3.3 0.2 - - - -
92P GLU* 1.3 76.1 - - - +
94P THR* 1.3 51.2 + - - +
96P ARG* 3.2 8.1 + - + +
97P ARG* 2.8 36.1 + - - +
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Residues in contact with THR 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P LEU* 4.0 15.7 - - + +
90P GLN 3.0 19.3 + - - -
91P SER 3.6 4.9 - - - -
93P ARG* 1.3 74.7 - - - +
95P ALA* 1.3 57.8 + - - +
97P ARG* 3.2 9.0 + - - +
98P LEU* 2.9 26.7 + - - +
122P PHE* 3.6 18.6 - - + -
137P LEU* 4.0 22.1 - - + +
138P PRO* 3.5 31.3 + - + +
139P HIS* 3.7 10.6 - - - -
140P VAL* 4.9 0.4 - - + -
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Residues in contact with ALA 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P SER 3.0 13.2 + - - +
92P GLU* 3.7 9.4 - - - +
93P ARG 3.3 0.2 - - - -
94P THR* 1.3 73.9 - - - +
96P ARG* 1.3 65.7 + - - +
98P LEU* 3.1 5.1 + - - +
99P GLN* 3.0 24.3 + - - +
111P ILE* 4.1 24.0 - - + +
114P VAL* 5.1 3.6 - - + -
122P PHE* 3.7 36.5 - - + -
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Residues in contact with ARG 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P GLU* 2.9 40.7 + - - +
93P ARG* 3.5 8.3 - - + +
95P ALA* 1.3 76.1 - - - +
97P ARG* 1.3 62.2 + - - +
99P GLN* 3.2 19.5 + - + +
100P ALA* 3.0 24.9 + - - +
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Residues in contact with ARG 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P ARG 2.8 17.1 + - - +
94P THR* 3.4 11.9 - - - +
96P ARG* 1.3 72.9 - - - +
98P LEU* 1.3 62.8 + - - +
100P ALA* 3.9 4.5 - - - +
101P GLN* 2.9 51.2 + - - +
137P LEU* 4.0 7.3 - - + +
138P PRO* 3.8 30.9 - - - +
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Residues in contact with LEU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P VAL* 5.0 0.9 - - + -
94P THR 2.9 13.1 + - - +
95P ALA* 3.1 10.5 + - - +
97P ARG* 1.3 75.5 - - - +
99P GLN* 1.3 53.8 + - - +
101P GLN* 3.5 2.5 - - - +
102P ALA* 2.8 40.0 + - + +
109P THR* 4.5 6.7 - - + +
111P ILE* 4.9 2.0 - - + -
122P PHE* 3.8 26.9 - - + -
124P VAL* 4.0 22.7 - - + -
126P MET* 4.1 15.5 - - - -
130P LEU* 5.1 2.5 - - + +
133P LEU* 4.5 16.8 - - + -
134P ALA* 4.1 25.1 - - + -
137P LEU* 3.9 19.7 - - + +
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Residues in contact with GLN 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P ALA 3.0 10.0 + - - +
96P ARG* 3.4 25.9 + - + +
98P LEU* 1.3 76.9 - - - +
100P ALA* 1.3 56.8 + - - +
102P ALA* 3.3 2.6 + - - +
103P ALA* 2.9 29.3 + - - +
107P TYR 4.8 0.7 - - - +
108P LEU* 5.6 1.5 - - + +
109P THR* 3.2 39.7 + - - +
110P LYS* 4.5 0.6 - - - +
111P ILE* 3.4 32.5 - - + +
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Residues in contact with ALA 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P ARG 3.0 16.0 + - - +
97P ARG* 3.9 4.7 - - - +
99P GLN* 1.3 72.7 - - - +
101P GLN* 1.3 61.1 + - - +
103P ALA* 3.4 6.7 + - - +
104P ARG* 3.0 30.8 + - - +
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Residues in contact with GLN 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P ARG* 2.9 52.9 + - - +
98P LEU* 3.5 5.1 - - - +
100P ALA* 1.3 78.8 - - - +
102P ALA* 1.3 58.5 + - - +
104P ARG* 3.7 10.7 - - - +
105P ARG* 2.8 44.2 + - - +
133P LEU* 3.3 35.7 + - + +
136P LYS* 6.0 1.2 - - - +
137P LEU* 3.9 19.0 - - - +
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Residues in contact with ALA 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P LEU* 2.8 19.1 + - + +
99P GLN 3.3 2.0 + - - +
101P GLN* 1.3 74.6 - - - +
103P ALA* 1.3 59.5 + - - +
104P ARG 3.2 1.6 - - - -
105P ARG* 2.9 21.4 + - - +
106P GLY 3.2 0.2 + - - -
107P TYR* 3.1 23.2 + - - +
109P THR* 3.4 28.5 - - + -
130P LEU* 3.9 25.6 - - + -
133P LEU* 4.6 2.7 - - + +
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Residues in contact with ALA 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN 2.9 17.9 + - - +
100P ALA* 3.6 7.9 - - - +
102P ALA* 1.3 69.5 - - - +
104P ARG* 1.3 58.0 + - - +
105P ARG 2.9 11.2 + - - -
106P GLY* 2.9 14.4 + - - +
107P TYR 3.5 11.1 + - - +
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Residues in contact with ARG 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P ALA 3.0 18.0 + - - +
101P GLN* 3.7 12.1 - - - +
103P ALA* 1.3 73.5 - - - +
105P ARG* 1.3 77.5 + - + +
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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