Contacts of the helix formed by residues 138 - 155 (chain T) in PDB entry 2X86
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 ASN 138 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P PHE* 3.4 9.4 - - - -
81T THR* 3.7 34.6 + - - +
84T TRP* 3.5 24.7 - - + -
118T ALA* 5.0 5.7 - - - +
136T PRO* 4.0 2.1 - - - +
137T LEU* 1.3 83.7 + - - +
139T VAL* 1.3 59.4 + - - +
140T PHE* 3.4 7.9 + - - +
141T GLY* 2.7 35.7 + - - -
142T TYR* 2.9 21.8 + - - +
268T LEU* 6.2 0.8 - - - +
271T ARG* 3.9 21.1 + - + +
401T ADP 5.1 2.2 + - - -
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Residues in contact with VAL 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P LEU* 4.2 11.2 - - + -
36P GLY* 3.8 24.7 - - - +
39P PHE* 3.8 12.7 - - + -
83T GLU 3.4 24.0 - - - +
84T TRP* 3.6 24.2 - - + -
86T GLY* 4.1 18.2 - - - -
89T MET* 3.8 15.3 - - + +
90T MET* 5.0 3.8 - - - -
138T ASN* 1.3 71.0 - - + +
140T PHE* 1.3 68.6 + - - +
142T TYR* 4.0 8.1 - - + -
143T SER* 2.9 22.7 + - - -
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Residues in contact with PHE 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T CYS 3.4 27.1 - - - -
79T SER* 3.9 5.8 - - - -
80T SER 3.7 21.8 - - - +
81T THR* 3.8 21.7 + - + -
83T GLU 4.9 0.6 + - - +
89T MET* 3.9 10.3 - - + -
93T ASN* 4.0 6.1 - - - -
116T SER* 3.9 12.8 - - - -
118T ALA* 4.1 6.1 - - + -
138T ASN* 3.2 9.1 + - - +
139T VAL* 1.3 82.4 - - - +
141T GLY* 1.3 67.2 + - - +
143T SER* 2.6 24.3 + - - -
144T LYS* 3.2 28.1 + - + +
400T NAP 3.3 26.7 - - - -
402T BMA 3.5 32.1 - - - -
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Residues in contact with GLY 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118T ALA* 4.4 14.1 - - - -
119T THR* 3.9 2.4 - - - +
136T PRO* 3.4 16.7 - - - +
138T ASN* 2.7 22.4 + - - -
140T PHE* 1.3 81.0 - - - +
142T TYR* 1.3 57.8 + - - +
144T LYS* 3.2 6.7 + - - +
145T PHE* 2.8 29.8 + - - +
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Residues in contact with TYR 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P LEU* 4.8 7.2 - - + -
39P PHE* 3.8 39.0 - + + -
42P LEU* 3.5 34.1 + - + +
43P VAL* 4.2 18.6 - - - -
47P ILE* 3.5 23.2 - - - +
50P TYR* 5.7 1.8 - + + -
90T MET* 4.1 29.4 - - + -
136T PRO* 3.6 12.0 - - + +
138T ASN 2.9 6.6 + - - +
139T VAL* 3.5 10.3 - - + +
140T PHE 3.2 0.2 - - - -
141T GLY* 1.3 77.2 - - - +
143T SER* 1.3 56.5 + - - +
145T PHE* 3.2 26.1 + + - +
146T LEU* 2.9 44.6 + - + +
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Residues in contact with SER 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89T MET* 3.6 16.6 - - - +
90T MET* 3.9 22.2 - - - -
93T ASN* 3.2 33.0 + - - +
94T TYR* 4.1 12.4 + - - +
139T VAL 2.9 11.8 + - - -
140T PHE 2.6 19.3 + - - -
142T TYR* 1.3 76.8 - - - +
144T LYS* 1.3 62.2 + - - +
146T LEU 4.0 0.2 + - - -
147T PHE* 3.5 19.6 + - - +
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Residues in contact with LYS 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74T HIS 5.9 0.2 + - - -
76T GLY 5.1 1.0 + - - -
77T ALA* 3.6 13.8 - - - +
93T ASN* 4.6 8.0 - - + +
114T ALA* 3.0 25.5 + - - +
115T SER* 4.1 11.0 - - - +
116T SER* 4.2 11.4 - - - +
119T THR* 3.9 14.1 - - + -
140T PHE* 3.2 31.4 + - + +
141T GLY* 3.2 7.6 + - - +
142T TYR 3.1 0.4 - - - -
143T SER* 1.3 83.3 + - - +
145T PHE* 1.3 66.5 + - - +
147T PHE* 3.1 9.4 + - + +
148T ASP* 3.0 25.1 + - - +
400T NAP 2.9 41.6 + - - -
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Residues in contact with PHE 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P LEU 5.7 0.2 - - - -
43P VAL 4.6 4.9 - - - -
45P LEU 4.9 4.0 - - - -
46P ASN* 5.4 0.2 - - - -
119T THR* 3.5 13.6 - - + +
131T ARG* 3.5 43.5 - - + -
134T GLU* 3.2 39.9 - - + -
136T PRO* 3.9 17.7 - - + -
141T GLY 2.8 16.6 + - - +
142T TYR* 3.5 29.8 - + - +
144T LYS* 1.3 75.8 - - - +
146T LEU* 1.3 74.2 + - + +
148T ASP* 3.0 7.9 + - - +
149T GLU* 3.0 45.7 + - + +
152T ARG* 4.9 0.7 - - - -
166T ARG* 5.6 0.7 - - - -
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Residues in contact with LEU 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P ILE* 4.0 24.2 - - + +
48P ALA 5.6 1.3 - - - +
49P ASP* 5.5 2.2 - - - -
50P TYR* 3.5 34.1 - - + +
90T MET* 3.7 14.4 - - + -
94T TYR* 3.5 31.1 + - + +
142T TYR* 2.9 42.5 + - + +
143T SER 4.5 0.4 - - - +
145T PHE* 1.3 89.7 - - + +
147T PHE* 1.3 57.9 + - - +
149T GLU* 3.3 11.3 + - + +
150T TYR* 2.9 22.5 + - - +
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Residues in contact with PHE 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T ASN 5.6 0.2 - - - +
94T TYR* 3.6 18.1 - + + -
97T SER* 3.6 36.8 - - - -
98T LYS* 3.5 34.1 - - + -
101T LEU* 4.0 17.0 - - + -
111T PHE* 4.0 7.9 - + - -
113T TYR* 3.7 39.7 - + - -
143T SER 3.5 12.7 + - - +
144T LYS* 3.1 11.4 + - + +
146T LEU* 1.3 77.4 - - - +
148T ASP* 1.3 60.4 + - - +
150T TYR* 2.9 9.8 + + + +
151T VAL* 2.8 47.8 + - + +
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Residues in contact with ASP 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113T TYR* 2.7 41.5 + - - -
115T SER* 2.6 29.2 + - - -
119T THR* 4.2 3.8 - - - +
144T LYS 3.0 15.1 + - - +
145T PHE 3.0 7.8 + - - +
147T PHE* 1.3 75.3 - - - +
149T GLU* 1.3 56.7 + - - +
151T VAL* 3.2 2.6 + - - +
152T ARG* 2.8 39.9 + - - +
166T ARG* 2.8 26.1 + - - +
232T ILE* 3.8 14.2 - - + +
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Residues in contact with GLU 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ASN* 4.6 7.3 - - - +
47P ILE 5.1 9.6 - - - +
131T ARG* 3.7 26.2 - - - +
145T PHE* 3.0 39.9 + - + +
146T LEU* 3.4 17.5 - - + +
148T ASP* 1.3 76.6 - - - +
150T TYR* 1.3 63.1 + - - +
152T ARG* 2.9 40.6 + - - +
153T GLN* 3.2 31.1 + - - +
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Residues in contact with TYR 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P ALA 4.1 11.4 - - - +
49P ASP* 4.3 11.2 - - + -
94T TYR* 3.7 18.8 - - + +
98T LYS* 3.6 32.1 + - + +
101T LEU* 4.0 23.6 - - + -
102T HIS* 2.6 37.4 + + - -
146T LEU 2.9 13.4 + - - +
147T PHE* 3.2 14.8 - + + +
149T GLU* 1.3 76.0 - - - +
151T VAL* 1.3 66.0 + - - +
153T GLN* 3.1 27.9 + - + +
154T ILE* 3.2 26.2 + - + +
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Residues in contact with VAL 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101T LEU* 4.3 8.7 - - + -
113T TYR* 3.5 27.8 - - + +
147T PHE* 2.8 44.6 + - + +
148T ASP 3.5 7.0 - - - +
150T TYR* 1.3 73.5 - - - +
152T ARG* 1.3 58.7 + - - +
154T ILE* 2.9 10.3 + - - +
155T LEU* 2.8 44.9 + - + +
162T ILE* 3.7 26.2 - - + -
231T GLY 5.8 0.4 - - - +
232T ILE* 4.4 8.1 - - + -
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Residues in contact with ARG 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ASP* 6.2 0.2 - - - +
129T GLU* 3.5 24.4 + - - +
130T SER* 3.8 2.0 - - - +
131T ARG* 3.9 10.5 - - - +
134T GLU* 2.5 45.7 + - - -
145T PHE* 4.6 0.6 - - - -
148T ASP* 2.8 23.2 + - - +
149T GLU* 2.9 34.2 + - - +
150T TYR 3.2 0.4 - - - -
151T VAL* 1.3 76.8 - - - +
153T GLN* 1.3 60.8 + - - +
155T LEU* 4.1 12.0 - - + +
156T PRO* 3.4 19.4 - - - +
166T ARG* 3.9 6.0 - - - +
232T ILE* 3.9 26.7 - - + +
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Residues in contact with GLN 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P ILE 4.5 3.4 + - - -
48P ALA* 2.9 46.1 + - - +
149T GLU* 3.2 23.2 + - - +
150T TYR* 3.1 23.8 + - + +
152T ARG* 1.3 76.4 - - - +
154T ILE* 1.3 66.0 + - + +
156T PRO* 3.7 8.3 - - - +
157T GLU* 5.3 2.4 + - - +
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Residues in contact with ILE 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101T LEU* 4.3 6.1 - - + -
102T HIS* 4.5 15.5 - - + -
105T LEU* 3.6 27.6 - - + -
150T TYR* 3.2 38.1 + - + +
151T VAL* 2.9 10.2 + - - +
153T GLN* 1.3 82.3 - - + +
155T LEU* 1.3 66.0 + - - +
156T PRO 3.4 0.2 - - - -
157T GLU* 3.0 18.7 + - - +
158T ALA* 3.2 10.7 + - + +
162T ILE* 3.9 16.6 - - + -
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Residues in contact with LEU 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ASP* 5.7 8.7 - - + +
151T VAL* 2.8 32.7 + - + +
152T ARG* 4.1 14.8 - - + +
154T ILE* 1.3 75.1 - - - +
156T PRO* 1.4 71.7 - - + +
157T GLU 3.0 1.2 + - - -
158T ALA* 3.2 20.7 + - + +
162T ILE* 4.0 31.0 - - + +
230T SER* 4.1 21.3 - - - -
231T GLY* 4.2 19.3 - - - -
232T ILE* 5.0 3.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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