Contacts of the helix formed by residues 87 - 100 (chain K) in PDB entry 2I2R
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 ASP 87 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92J ARG* 3.0 29.1 + - - -
96J ASN* 2.9 43.8 + - - +
99J ARG* 4.2 0.8 - - - +
46K VAL* 3.8 1.6 - - - +
86K ARG* 1.3 77.6 - - - +
88K PRO* 1.3 68.7 - - - +
89K GLU* 3.2 4.2 + - - +
90K VAL* 2.5 41.7 + - + +
91K PHE* 3.8 15.1 + - - +
109K GLU* 4.7 1.1 - - - -
117K GLU* 4.0 18.5 + - + +
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Residues in contact with PRO 88 (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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49J ARG* 4.2 17.9 - - - +
51J PHE* 5.0 2.7 - - + -
92J ARG* 4.4 14.1 - - + -
96J ASN* 4.3 5.2 - - - +
99J ARG* 4.6 2.0 - - - +
46K VAL* 3.5 30.5 - - + +
47K SER* 3.8 15.9 - - - +
49K ARG* 3.8 22.4 - - + +
51K PHE* 3.5 11.2 - - + -
86K ARG 3.5 0.4 - - - -
87K ASP* 1.3 91.1 - - - +
89K GLU* 1.3 70.9 + - - +
91K PHE* 3.3 14.2 - - - +
92K ARG 3.5 3.6 + - - -
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Residues in contact with GLU 89 (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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89J GLU* 5.7 0.4 - - - +
92J ARG* 3.3 39.7 - - - +
49K ARG* 4.3 8.7 + - - -
87K ASP* 3.2 3.9 + - - +
88K PRO* 1.3 79.6 - - - +
90K VAL* 1.3 69.2 + - - +
92K ARG* 2.6 66.4 + - - +
93K CYS* 4.1 1.7 + - - -
108K TYR* 2.7 22.7 + - + +
109K GLU* 4.5 5.2 - - + +
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Residues in contact with VAL 90 (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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87K ASP* 2.5 18.5 + - - +
89K GLU* 1.3 72.9 - - - +
91K PHE* 1.3 53.5 + - - +
93K CYS* 2.8 32.8 + - - +
94K VAL* 3.3 17.2 + - + -
106K PRO* 5.6 1.3 - - + -
109K GLU* 3.6 27.1 - - + +
113K ALA* 4.7 2.2 - - + +
114K TYR* 3.9 41.3 - - + +
117K GLU* 3.4 38.6 - - + +
118K LEU* 5.3 0.4 - - + +
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Residues in contact with PHE 91 (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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44K LEU* 3.5 31.6 - - + -
46K VAL* 3.6 23.1 - - + -
51K PHE* 3.8 32.8 - + - -
66K LEU* 3.9 15.0 - - + -
84K PHE* 4.3 6.7 - + - -
87K ASP 3.8 12.6 + - - +
88K PRO* 3.3 15.7 + - + +
90K VAL* 1.3 77.9 - - - +
92K ARG* 1.3 52.4 + - - +
93K CYS 3.2 0.2 - - - -
94K VAL* 3.7 10.3 - - + -
95K LEU* 2.8 46.5 + - + +
121K TYR* 3.2 41.2 + + - +
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Residues in contact with ARG 92 (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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49K ARG* 5.0 5.4 - - - +
51K PHE* 4.1 23.7 - - + -
88K PRO 3.5 2.4 + - - -
89K GLU* 2.6 56.1 + - - +
91K PHE* 1.3 79.6 - - - +
93K CYS* 1.3 64.1 + - - +
95K LEU* 3.7 2.4 - - - +
96K ASN* 2.8 41.6 + - - +
99K ARG* 6.0 0.2 - - - +
106K PRO* 5.7 1.2 - - - +
108K TYR* 3.4 12.5 + - - -
87L ASP* 3.1 22.6 + - - +
88L PRO* 4.3 17.9 - - + -
89L GLU* 3.3 27.8 - - - +
108L TYR* 5.7 1.0 - - - -
109L GLU* 3.0 32.5 + - - -
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Residues in contact with CYS 93 (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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89K GLU 4.8 1.3 - - - -
90K VAL* 2.8 18.8 + - - +
92K ARG* 1.3 84.3 - - - +
94K VAL* 1.3 70.3 + - + +
96K ASN* 3.1 6.7 + - - +
97K PHE* 2.7 25.6 + - - +
103K LEU* 4.3 11.3 - - + +
104K HIS* 4.1 18.1 + - + +
106K PRO* 3.8 35.7 - - - -
108K TYR* 5.6 0.4 - - - -
114K TYR* 4.6 7.6 - - + -
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Residues in contact with VAL 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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66K LEU* 4.3 7.4 - - + -
90K VAL* 3.3 17.2 + - + +
91K PHE* 3.7 11.4 - - + +
93K CYS* 1.3 79.2 - - + +
95K LEU* 1.3 63.2 + - - +
97K PHE* 3.2 10.8 + - - +
98K TYR* 3.1 27.3 - - + -
103K LEU* 4.7 2.2 - - - +
118K LEU* 4.3 22.4 - - + -
121K TYR* 3.8 48.7 - - + -
123K ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 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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44K LEU* 4.5 9.9 - - + -
51K PHE* 4.0 29.2 - - + -
52K GLN 4.6 0.7 - - - +
53K THR* 4.2 18.4 - - + +
58K LEU* 3.8 28.9 - - + -
66K LEU* 5.8 1.3 - - + -
91K PHE* 2.8 35.0 + - + +
92K ARG* 3.8 4.5 - - - +
94K VAL* 1.3 70.7 - - - +
96K ASN* 1.3 53.4 + - - +
98K TYR* 2.7 37.9 + - + +
99K ARG* 3.3 41.4 + - + +
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Residues in contact with ASN 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 ARG* 2.8 31.2 + - - +
93K CYS* 3.1 6.9 + - - +
95K LEU* 1.3 71.7 - - - +
97K PHE* 1.3 61.5 + - - +
99K ARG* 3.3 29.7 - - - +
100K THR* 3.2 33.4 + - - +
102K LYS 4.3 2.5 - - - +
104K HIS* 6.0 5.2 - - + -
87L ASP* 2.8 50.4 + - - +
88L PRO* 4.1 3.4 - - - +
117L GLU* 4.7 3.1 - - - +
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Residues in contact with PHE 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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61K TYR* 3.4 51.3 - + + -
64K THR* 5.9 0.9 - - + -
93K CYS 2.7 15.0 + - - +
94K VAL* 3.4 9.6 - - - +
95K LEU 3.0 0.4 + - - -
96K ASN* 1.3 71.1 - - - +
98K TYR* 1.3 77.1 + + - +
99K ARG 3.1 0.2 - - - -
100K THR 2.5 19.1 - - - +
101K GLY 3.2 27.9 - - - +
102K LYS 3.5 9.8 + - - +
103K LEU* 3.2 40.4 - - + -
123K ILE* 4.3 20.2 - - + -
127K ILE* 3.9 34.3 - - + -
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Residues in contact with TYR 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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57K THR* 3.4 25.7 - - + +
58K LEU* 3.2 43.7 - - + -
60K ARG* 2.9 31.0 + - - -
61K TYR* 4.2 20.0 - + + -
64K THR* 2.4 37.3 + - - -
66K LEU* 3.6 20.1 + - + +
67K GLY 3.5 13.0 + - - -
94K VAL* 3.1 42.2 - - + -
95K LEU* 2.7 16.3 + - + +
97K PHE* 1.3 80.6 - + - +
99K ARG* 1.3 57.4 + - - +
123K ILE* 4.0 10.0 - - + +
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Residues in contact with ARG 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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51K PHE* 5.7 0.8 - - - -
52K GLN 3.3 5.1 + - - -
53K THR* 4.1 1.0 + - - +
57K THR* 3.9 17.5 - - + -
60K ARG* 4.1 15.8 + - - +
92K ARG* 6.0 0.2 - - - +
95K LEU* 3.3 44.2 + - + +
96K ASN* 3.3 37.6 - - - +
97K PHE 3.1 2.4 - - - -
98K TYR* 1.3 80.2 - - - +
100K THR* 1.3 62.0 + - - +
101K GLY 4.1 0.3 + - - -
47L SER* 2.6 37.0 + - - -
85L ASP* 2.7 43.0 + - - +
86L ARG* 3.6 16.8 + - - +
87L ASP* 4.2 0.6 - - - +
88L PRO* 4.6 1.6 - - - +
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Residues in contact with THR 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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60K ARG* 6.3 0.7 - - - -
96K ASN* 3.2 18.7 + - - +
97K PHE 2.5 27.8 - - - +
98K TYR 4.8 0.2 - - - -
99K ARG* 1.3 78.9 - - - +
101K GLY* 1.3 58.4 + - - +
102K LYS* 3.0 20.9 + - - +
104K HIS* 4.5 7.4 + - - -
86L ARG* 4.7 15.9 - - - +
116L ASP* 3.8 28.3 - - + +
117L GLU* 5.2 4.7 - - - +
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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
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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