Contacts of the strand formed by residues 18 - 26 (chain B) in PDB entry 2HEI
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 ILE 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS* 1.3 75.6 - - - +
19B CYS* 1.3 68.7 + - - +
20B GLN* 3.8 5.5 + - + +
68B THR* 3.3 29.8 - - + +
70B LYS* 4.1 34.1 - - + +
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Residues in contact with CYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 6.0 0.9 - - + -
17B LYS* 3.8 3.8 + - - -
18B ILE* 1.3 73.0 - - - +
20B GLN* 1.3 60.2 + - - +
21B PHE* 3.5 25.9 - - + -
67B THR* 4.3 17.0 - - - -
68B THR 3.1 7.5 + - - +
69B VAL* 3.3 9.5 - - + -
70B LYS* 2.8 25.1 + - - +
182B PRO 4.2 15.0 - - - -
183B LYS* 4.4 14.1 - - - -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 2.9 39.7 + - - +
82A TYR* 2.7 35.4 + - - -
18B ILE* 3.8 6.5 + - + +
19B CYS* 1.3 73.9 - - - +
21B PHE* 1.3 81.6 + - - +
22B LYS* 4.2 1.8 - - - +
59B THR* 5.9 0.2 - - + -
70B LYS* 3.1 34.3 - - + +
72B GLU* 3.7 25.5 + - + +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.7 33.9 - + - -
19B CYS* 3.5 27.6 - - + -
20B GLN* 1.3 80.8 + - - +
22B LYS* 1.3 56.5 + - - +
69B VAL* 3.5 33.2 - - + -
70B LYS 2.7 9.6 + - - +
71B PHE* 3.4 9.3 - - + -
72B GLU 2.8 31.2 + - - -
94B GLN* 3.5 26.5 - - + +
95B ALA* 5.8 0.4 - - + +
181B LEU* 3.8 27.1 - - + -
182B PRO* 3.4 39.0 - - + -
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 4.8 0.2 + - - -
20B GLN* 4.2 2.0 - - - +
21B PHE* 1.3 72.7 - - - +
23B LEU* 1.3 62.8 + - - +
24B VAL* 4.3 1.6 - - - -
72B GLU* 3.4 17.5 - - + +
74B TRP* 3.5 48.0 - - + +
88B MET 3.4 12.1 + - - -
89B TYR 3.0 26.0 + - - -
91B ARG* 2.7 31.0 + - - +
92B GLY 3.2 24.7 - - - +
93B ALA* 3.6 8.1 - - + -
94B GLN* 2.9 34.8 + - - +
95B ALA* 3.3 6.9 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE 4.1 0.2 + - - -
22B LYS* 1.3 75.7 - - - +
24B VAL* 1.3 66.9 + - - +
25B LEU* 3.5 28.9 - - + -
71B PHE* 3.9 34.8 - - + -
72B GLU 2.9 8.2 + - - +
73B ILE* 3.3 9.1 - - + -
74B TRP* 2.8 32.6 + - - +
95B ALA* 3.2 24.5 - - + +
96B ALA* 4.4 0.9 - - - +
97B ILE* 4.0 11.9 - - + -
174B PHE* 3.9 22.2 - - + -
177B ILE* 4.1 15.9 - - + -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 4.3 6.7 - - - -
23B LEU* 1.3 82.1 - - - +
25B LEU* 1.3 64.0 + - - +
26B LEU* 4.1 13.2 + - + -
74B TRP* 3.5 9.6 - - + +
76B THR* 3.9 25.1 - - + -
89B TYR* 3.3 36.1 - - + +
90B TYR* 4.4 11.2 - - + -
93B ALA* 3.8 17.3 - - + -
95B ALA 3.1 7.6 + - - +
96B ALA* 3.1 11.0 - - + +
97B ILE 2.9 24.6 + - - +
126B ILE* 6.1 0.2 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.5 16.2 - - + -
24B VAL* 1.3 71.7 - - - +
26B LEU* 1.3 55.8 + - - +
33B LYS* 3.7 31.8 - - + +
36B LEU* 4.5 9.4 - - + -
37B VAL* 3.5 21.5 - - + +
73B ILE* 3.2 35.0 - - + -
74B TRP 2.9 12.9 + - - +
75B ASP* 4.6 4.7 - - - +
76B THR* 2.6 38.2 + - - +
97B ILE* 3.4 18.8 - - + -
99B VAL* 4.3 13.5 - - + -
174B PHE* 5.0 4.0 - - + -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 4.1 9.9 - - + +
25B LEU* 1.3 74.1 - - - +
27B GLY* 1.3 58.2 + - - +
33B LYS* 3.6 5.6 - - - +
76B THR* 3.7 29.6 - - + +
90B TYR* 3.0 32.8 - - + +
96B ALA* 4.8 3.6 - - + -
97B ILE 2.8 10.4 + - - +
98B VAL* 4.2 5.2 - - + -
99B VAL* 2.8 31.3 + - - +
114B TRP* 4.0 24.9 - - + +
118B LEU* 3.7 34.3 - - + -
302B D1D 3.9 16.6 - - + +
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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