Contacts of the helix formed by residues 19 - 31 (chain B) in PDB entry 1CI1
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 GLU 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP* 3.7 7.8 + - - +
87A TYR* 6.3 4.4 - - + -
18B SER* 1.3 71.8 - - - +
20B SER* 1.3 63.6 + - - +
23B VAL* 3.0 36.1 + - + +
48B HIS* 5.0 2.0 + - - -
51B MET* 3.9 31.7 - - + -
55B ARG* 4.2 19.5 + - - +
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Residues in contact with SER 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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86A ASP* 5.2 1.8 + - - -
18B SER* 3.2 10.5 + - - -
19B GLU* 1.3 81.2 + - - +
21B LEU* 1.3 60.4 + - - +
24B PRO* 3.2 23.3 - - - +
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Residues in contact with LEU 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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16B ASN* 5.5 0.7 - - + -
17B GLY* 3.9 24.5 - - - +
18B SER* 3.1 13.4 + - - +
20B SER* 1.3 81.4 + - - +
22B LEU* 1.3 68.1 + - + +
24B PRO* 3.4 9.6 - - - +
25B LEU* 3.6 14.4 + - + +
239B LEU* 3.9 43.7 - - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TRP* 3.9 37.9 - - + -
16B ASN 5.2 0.2 - - - +
17B GLY* 4.2 6.1 - - - -
18B SER 2.8 26.1 + - - +
19B GLU 4.2 0.4 - - - +
21B LEU* 1.3 95.4 - - + +
23B VAL* 1.3 60.3 + - - +
25B LEU* 3.1 6.4 + - + +
26B ILE* 2.9 37.4 + - + +
48B HIS* 3.6 42.0 - - + +
51B MET* 4.4 15.0 - - + -
52B THR* 5.1 1.3 - - - +
239B LEU* 4.3 9.4 - - + -
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Residues in contact with VAL 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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19B GLU* 3.0 24.7 + - + +
20B SER* 5.6 0.4 - - - -
22B LEU* 1.3 73.4 - - - +
24B PRO* 1.3 71.5 - - + +
26B ILE* 3.3 7.3 + - - +
27B GLU* 2.9 46.3 + - + +
51B MET* 3.3 27.6 - - + -
55B ARG* 3.7 28.9 - - - +
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Residues in contact with PRO 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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20B SER 3.2 26.7 - - - +
21B LEU 3.4 9.2 - - - +
23B VAL* 1.3 98.1 - - + +
25B LEU* 1.3 55.0 + - - +
27B GLU* 3.4 15.4 + - - +
28B THR* 3.0 32.0 + - - -
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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
----------------------------------------------------------
13B TRP* 3.4 34.5 - - + +
21B LEU* 3.6 13.4 + - + +
22B LEU* 3.1 12.2 + - + +
24B PRO* 1.3 78.3 - - - +
26B ILE* 1.3 65.4 + - - +
28B THR* 3.2 10.0 + - + +
29B LEU* 3.1 41.9 + - + +
238B SER 3.7 16.2 - - - +
239B LEU* 4.1 21.5 - - + +
240B LYS 4.1 26.0 - - - +
241B PRO* 4.6 4.7 - - + -
243B PHE* 5.9 0.2 - - + -
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Residues in contact with ILE 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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13B TRP* 4.6 14.6 - - + -
22B LEU* 2.9 26.8 + - + +
23B VAL* 3.7 4.9 - - - +
25B LEU* 1.3 75.9 - - - +
27B GLU* 1.3 53.4 + - + +
29B LEU* 3.2 9.7 + - + +
30B ASN* 2.7 60.9 + - - +
51B MET* 4.5 6.3 - - + +
52B THR* 3.9 38.8 - - + +
55B ARG* 3.9 34.3 - - + +
56B LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 27 (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 VAL* 2.9 34.8 + - + +
24B PRO* 3.5 16.3 - - - +
26B ILE* 1.3 77.1 - - + +
28B THR* 1.3 57.3 + - - +
30B ASN* 3.3 10.6 + - - +
31B ALA* 2.8 31.4 + - - +
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Residues in contact with THR 28 (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 PRO 3.0 15.5 + - - -
25B LEU* 3.4 14.3 - - + +
27B GLU* 1.3 76.5 - - - +
29B LEU* 1.3 63.4 + - + +
31B ALA* 3.0 16.9 + - - +
32B ALA* 3.1 13.7 + - - +
241B PRO* 4.5 24.8 - - + +
244B VAL* 4.1 20.9 - - + -
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Residues in contact with LEU 29 (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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13B TRP* 4.7 12.6 - - + -
25B LEU* 3.1 28.0 + - + +
26B ILE* 3.6 13.0 - - + +
28B THR* 1.3 77.3 - - + +
30B ASN* 1.3 58.9 + - - +
32B ALA* 3.4 10.2 + - - +
34B PHE* 6.0 0.4 - - + -
42B VAL* 4.1 16.4 - - + -
56B LEU* 4.8 10.3 - - + -
58B ASN* 2.8 28.1 + - - -
61B PHE* 4.1 31.4 - - + -
238B SER 6.0 0.2 - - - +
241B PRO* 6.5 0.2 - - + -
243B PHE* 4.0 27.4 - - + -
244B VAL* 4.3 17.3 - - + -
247B ILE* 5.1 1.1 - - + -
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Residues in contact with ASN 30 (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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26B ILE* 2.7 30.8 + - - +
27B GLU* 3.6 9.5 - - - +
29B LEU* 1.3 74.0 - - - +
31B ALA* 1.3 61.1 + - - +
32B ALA 3.4 5.0 + - - +
55B ARG* 2.8 26.9 + - - +
56B LEU* 3.1 17.5 - - - +
57B THR* 2.9 39.1 + - - +
58B ASN* 3.4 9.3 + - - +
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Residues in contact with ALA 31 (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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27B GLU 2.8 17.2 + - - +
28B THR* 3.0 8.0 + - - +
30B ASN* 1.3 78.2 - - - +
32B ALA* 1.3 58.7 + - - +
33B THR* 3.9 6.2 + - - -
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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