Contacts of the helix formed by residues 138 - 155 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K THR* 3.7 35.1 + - - +
84K TRP* 3.5 24.5 - - + -
118K ALA* 5.1 5.6 - - - +
136K PRO* 4.0 1.9 - - - +
137K LEU* 1.3 84.4 - - - +
139K VAL* 1.3 59.5 + - - +
140K PHE* 3.4 9.2 + - - +
141K GLY* 2.7 35.3 + - - -
142K TYR* 2.9 22.2 + - - +
268K LEU* 6.3 1.0 - - - +
271K ARG* 3.9 20.7 + - + +
401K ADP 5.2 1.6 + - - -
39L PHE* 3.4 9.2 - - - -
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Residues in contact with VAL 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K GLU 3.4 23.8 - - - +
84K TRP* 3.6 24.9 - - + -
86K GLY* 4.1 19.1 - - - -
89K MET* 3.8 15.5 - - + +
90K MET* 5.0 4.3 - - - -
138K ASN* 1.3 73.0 - - + +
140K PHE* 1.3 68.8 + - - +
142K TYR* 4.0 9.0 - - + -
143K SER* 2.9 22.9 + - - -
33L LEU* 4.2 14.4 - - + -
36L GLY* 3.8 24.0 - - - +
39L PHE* 3.9 7.4 - - + -
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Residues in contact with PHE 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K CYS 3.4 26.5 - - - -
79K SER* 3.9 5.6 - - - -
80K SER 3.7 22.2 - - - +
81K THR* 3.8 20.6 + - + -
83K GLU 4.9 0.4 + - - -
89K MET* 3.9 10.5 - - + -
93K ASN* 4.0 5.4 - - - -
116K SER* 3.9 13.9 - - - -
118K ALA* 4.1 5.8 - - + -
138K ASN* 3.2 8.2 + - - +
139K VAL* 1.3 81.6 - - - +
141K GLY* 1.3 67.7 + - - +
143K SER* 2.6 24.2 + - - -
144K LYS* 3.2 27.1 + - + +
400K NAP 3.2 27.6 - - - -
402K BMA 3.7 31.2 - - - -
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Residues in contact with GLY 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K ALA* 4.4 14.6 - - - -
119K THR* 3.9 2.8 - - - +
136K PRO* 3.4 16.8 - - - +
138K ASN* 2.7 22.1 + - - -
140K PHE* 1.3 82.0 - - - +
142K TYR* 1.3 57.6 + - - +
144K LYS* 3.2 5.9 + - - +
145K PHE* 2.8 29.8 + - - +
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Residues in contact with TYR 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K MET* 4.1 29.2 - - + -
136K PRO* 3.6 11.3 - - + +
138K ASN 2.9 6.6 + - - +
139K VAL* 3.5 9.9 - - + +
140K PHE 3.2 0.4 - - - -
141K GLY* 1.3 76.7 - - - +
143K SER* 1.3 57.0 + - - +
145K PHE* 3.2 25.3 + + - +
146K LEU* 2.9 45.5 + - + +
33L LEU* 4.8 6.7 - - + -
39L PHE* 3.7 39.7 - + + -
42L LEU* 3.4 33.2 + - + +
43L VAL* 4.2 18.6 - - - -
47L ILE* 3.6 22.0 - - - +
50L TYR* 5.8 1.8 - + + -
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Residues in contact with SER 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K MET* 3.6 15.9 - - - +
90K MET* 3.9 22.4 - - - -
93K ASN* 3.2 33.3 + - - +
94K TYR* 4.1 11.6 + - - +
139K VAL 2.9 12.7 + - - -
140K PHE 2.6 19.6 + - - -
142K TYR* 1.3 78.1 - - - +
144K LYS* 1.3 63.4 + - - +
147K PHE* 3.5 20.1 + - - +
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Residues in contact with LYS 144 (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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74K HIS 5.9 0.4 + - - -
76K GLY 5.0 1.0 + - - -
77K ALA* 3.6 14.1 - - - +
93K ASN* 4.6 8.0 - - + +
97K SER* 5.7 3.4 + - - -
114K ALA* 3.0 25.9 + - - +
115K SER* 4.1 11.2 - - - +
116K SER* 4.2 11.0 - - - +
119K THR* 3.9 13.9 - - + -
140K PHE* 3.7 31.0 - - + +
141K GLY* 3.2 7.8 + - - +
142K TYR 3.1 0.4 - - - -
143K SER* 1.3 84.0 + - - +
145K PHE* 1.3 65.8 + - - +
147K PHE* 3.1 7.7 + - + +
148K ASP* 3.0 25.2 + - - +
400K NAP 2.9 42.7 + - - -
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Residues in contact with PHE 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K THR* 3.5 13.8 - - + +
131K ARG* 3.5 43.3 - - + -
134K GLU* 3.2 39.3 - - + -
136K PRO* 3.9 16.6 - - + -
141K GLY 2.8 17.2 + - - +
142K TYR* 3.5 28.7 - + - +
144K LYS* 1.3 76.9 - - - +
146K LEU* 1.3 73.5 + - + +
148K ASP* 3.0 7.7 + - - +
149K GLU* 3.0 44.9 + - + +
152K ARG* 4.9 0.2 - - - -
166K ARG* 5.6 0.4 - - - -
42L LEU 5.6 0.2 - - - -
43L VAL 4.5 4.9 - - - -
45L LEU 4.9 4.5 - - - -
46L ASN* 5.4 0.2 - - - -
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Residues in contact with LEU 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K MET* 3.6 21.8 - - + -
94K TYR* 3.5 36.6 - - + +
142K TYR* 2.9 43.4 + - + +
145K PHE* 1.3 88.5 - - + +
147K PHE* 1.3 58.9 + - - +
149K GLU* 3.3 11.3 + - + +
150K TYR* 2.9 22.9 + - - +
47L ILE* 4.0 23.3 - - + +
48L ALA 5.7 1.6 - - - +
49L ASP 4.7 2.0 - - - +
50L TYR* 3.7 19.1 - - + +
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Residues in contact with PHE 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K ASN 5.6 0.2 - - - +
94K TYR* 3.6 17.6 - + + -
97K SER* 3.6 35.2 - - - -
98K LYS* 3.5 33.7 - - + -
101K LEU* 4.0 17.0 - - + -
111K PHE* 4.0 8.5 - + - -
113K TYR* 3.7 39.3 - + - -
114K ALA 5.8 0.2 - - - -
143K SER 3.5 12.9 + - - +
144K LYS* 3.1 11.2 + - + +
146K LEU* 1.3 78.3 - - - +
148K ASP* 1.3 60.5 + - - +
150K TYR* 2.9 9.4 + + + +
151K VAL* 2.8 46.5 + - + +
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Residues in contact with ASP 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K TYR* 2.7 41.9 + - - -
115K SER* 2.6 28.1 + - - -
119K THR* 4.2 4.2 - - - +
144K LYS 3.0 14.7 + - - +
145K PHE* 3.4 7.9 - - - +
147K PHE* 1.3 74.1 - - - +
149K GLU* 1.3 57.3 + - - +
151K VAL* 3.2 2.8 + - - +
152K ARG* 2.8 40.0 + - - +
166K ARG* 2.8 25.5 + - - +
232K ILE* 3.8 14.1 - - + +
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Residues in contact with GLU 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131K ARG* 3.7 25.3 - - - +
145K PHE* 3.0 39.4 + - + +
146K LEU* 3.4 17.3 - - + +
148K ASP* 1.3 76.9 - - - +
150K TYR* 1.3 62.9 + - - +
152K ARG* 2.9 39.2 + - - +
153K GLN* 3.2 32.0 + - - +
46L ASN* 4.4 9.4 - - - +
47L ILE 5.3 7.7 - - - +
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Residues in contact with TYR 150 (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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94K TYR* 3.7 18.8 - - + +
98K LYS* 3.6 31.4 + - + +
101K LEU* 4.0 18.8 - - + -
102K HIS* 2.6 37.2 + + - -
146K LEU 2.9 13.6 + - - +
147K PHE* 3.2 15.5 - + + +
149K GLU* 1.3 75.3 - - - +
151K VAL* 1.3 66.8 + - - +
153K GLN* 3.1 28.1 + - + +
154K ILE* 3.2 29.0 + - + +
48L ALA 4.0 12.3 - - - +
49L ASP* 4.4 10.8 - - + -
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Residues in contact with VAL 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K LEU* 4.3 8.1 - - + -
113K TYR* 3.5 28.3 - - + +
147K PHE* 2.8 45.6 + - + +
148K ASP 3.5 7.2 - - - +
150K TYR* 1.3 72.6 - - - +
152K ARG* 1.3 59.6 + - - +
154K ILE* 2.9 8.9 + - - +
155K LEU* 2.8 44.6 + - + +
162K ILE* 3.7 26.0 - - + +
231K GLY 5.8 0.7 - - - +
232K ILE* 4.4 8.1 - - + -
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Residues in contact with ARG 152 (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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129K GLU* 3.5 24.7 + - - +
130K SER* 3.8 2.0 - - - +
131K ARG* 3.8 11.1 - - - +
134K GLU* 2.5 45.2 + - - -
145K PHE* 4.6 0.6 - - - -
148K ASP* 2.8 22.6 + - - +
149K GLU* 2.9 33.4 + - - +
150K TYR 3.2 0.2 - - - -
151K VAL* 1.3 76.1 - - - +
153K GLN* 1.3 60.8 + - - +
155K LEU* 4.1 12.6 - - + +
156K PRO* 3.4 19.4 - - - +
166K ARG* 4.0 5.9 - - - +
232K ILE* 3.9 27.4 - - + +
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Residues in contact with GLN 153 (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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149K GLU* 3.2 24.5 + - - +
150K TYR* 3.1 24.0 + - + +
152K ARG* 1.3 77.3 - - + +
154K ILE* 1.3 65.2 + - + +
156K PRO* 3.7 9.0 - - - +
157K GLU* 5.2 2.4 + - - +
47L ILE 4.4 4.4 + - - -
48L ALA* 3.1 44.9 + - - +
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Residues in contact with ILE 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K LEU* 4.3 7.0 - - + -
102K HIS* 4.5 15.9 - - + -
105K LEU* 3.5 28.0 - - + -
150K TYR* 3.5 37.5 - - + +
151K VAL* 2.9 10.0 + - - +
153K GLN* 1.3 81.0 - - + +
155K LEU* 1.3 67.5 + - - +
157K GLU* 3.0 18.5 + - + +
158K ALA* 3.2 10.2 + - + +
162K ILE* 3.9 17.0 - - + -
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Residues in contact with LEU 155 (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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151K VAL* 2.8 31.2 + - + +
152K ARG* 4.1 15.3 - - + +
154K ILE* 1.3 75.2 - - - +
156K PRO* 1.4 69.7 - - + +
157K GLU 3.0 1.2 + - - -
158K ALA* 3.2 21.2 + - + +
162K ILE* 4.0 30.1 - - + +
230K SER* 4.1 21.3 - - - +
231K GLY* 4.3 19.1 - - - +
232K ILE* 5.1 2.7 - - + +
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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
------------------------------------------------------------
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