Contacts of the helix formed by residues 18 - 29 (chain B) in PDB entry 3SEA
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 GLY 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B SER 3.2 2.6 - - - -
17B VAL* 1.3 80.6 - - - +
19B LYS* 1.3 69.2 + - - +
20B SER 3.4 2.0 - - - -
22B LEU* 2.9 28.3 + - - +
84B VAL* 5.0 2.2 - - - -
119B ASN* 3.6 5.8 + - - -
179B GNP 3.1 36.5 + - - -
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Residues in contact with LYS 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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11B ILE* 3.8 28.4 - - + +
12B LEU* 3.5 5.4 - - - -
13B GLY* 3.5 31.6 + - - +
14B TYR 2.8 20.0 + - - -
17B VAL* 3.8 11.8 - - + +
18B GLY* 1.3 76.7 - - - +
20B SER* 1.3 61.7 + - - +
22B LEU* 3.8 3.3 - - - +
23B THR* 2.8 28.2 + - - -
60B ASP* 3.5 11.9 - - - +
61B THR 3.4 23.3 - - - -
62B ALA 4.3 1.1 - - - -
63B GLY* 4.0 2.7 - - - +
84B VAL* 4.2 9.9 - - + -
179B GNP 2.6 48.3 + - - +
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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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1B ACT 3.8 22.2 + - - -
19B LYS* 1.3 73.8 - - - +
21B SER* 1.3 61.8 + - - +
23B THR* 3.3 1.2 + - - -
24B ILE* 2.8 41.3 + - - +
35B ALA* 4.7 0.9 - - - -
38B THR* 2.8 4.7 + - - -
60B ASP* 2.4 27.4 + - - -
178B MG 2.2 29.6 - - - -
179B GNP 3.0 12.6 + - - -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 4.0 0.7 - - - -
19B LYS 3.4 0.4 - - - -
20B SER* 1.3 72.4 - - - +
22B LEU* 1.3 57.8 + - - +
24B ILE* 3.9 1.0 - - - +
25B GLN* 3.0 29.6 + - - +
30B GLN 4.7 1.9 - - - +
31B PHE* 4.1 9.1 - - - -
32B VAL* 3.5 30.2 + - - +
35B ALA* 4.7 1.0 - - - +
150B ALA* 3.5 12.7 - - - +
179B GNP 2.7 57.6 + - - -
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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
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11B ILE* 6.4 1.3 - - + -
18B GLY 2.9 17.7 + - - +
19B LYS* 3.8 3.4 - - - +
21B SER* 1.3 71.9 - - - +
23B THR* 1.3 66.9 + - - +
25B GLN* 3.3 4.4 + - - +
26B PHE* 3.1 19.4 + - - +
82B ILE* 5.8 0.4 - - + -
84B VAL* 4.8 13.2 - - + -
117B VAL* 4.0 14.6 - - + -
119B ASN* 3.7 17.9 - - + +
148B SER* 3.5 28.5 - - - +
149B SER 4.4 0.7 - - - -
150B ALA* 3.6 17.8 - - + +
156B ALA* 3.5 41.3 - - + +
159B VAL* 4.2 15.5 - - + -
160B PHE* 4.2 6.2 - - + -
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Residues in contact with THR 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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11B ILE* 3.8 21.9 - - + +
19B LYS 2.8 21.5 + - - -
20B SER* 3.8 5.8 - - - -
22B LEU* 1.3 79.1 - - - +
24B ILE* 1.3 57.2 + - - +
26B PHE* 3.2 3.8 + - - +
27B VAL* 2.8 29.7 + - + +
43B PHE* 3.8 29.2 - - + -
58B LEU* 3.9 28.3 - - + -
60B ASP* 4.4 6.2 + - + -
160B PHE* 3.8 14.3 - - + -
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Residues in contact with ILE 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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1B ACT 4.3 18.6 - - + -
20B SER* 2.8 29.0 + - - +
21B SER 4.1 2.0 - - - +
23B THR* 1.3 70.7 - - - +
25B GLN* 1.3 58.9 + - - +
27B VAL* 4.3 5.6 - - - +
28B GLU* 2.7 56.2 + - + +
29B GLY 3.3 2.9 + - - -
30B GLN* 3.9 8.5 - - + +
32B VAL* 3.8 40.4 - - + -
43B PHE* 4.2 27.6 - - + -
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Residues in contact with GLN 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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21B SER 3.0 19.6 + - - +
22B LEU 3.5 5.4 - - - +
23B THR 3.2 0.2 - - - -
24B ILE* 1.3 75.6 - - - +
26B PHE* 1.3 57.3 + - - +
29B GLY* 2.8 49.6 + - - +
30B GLN* 3.4 25.3 + - - +
31B PHE* 3.6 6.1 - - - +
150B ALA 2.8 32.5 + - - +
151B LYS 4.0 10.3 + - - -
153B ASN* 3.0 50.5 + - - +
156B ALA* 3.8 11.4 - - + -
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Residues in contact with PHE 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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22B LEU 3.1 6.5 + - - +
23B THR 3.2 6.3 + - - +
25B GLN* 1.3 79.6 - - - +
27B VAL* 1.3 65.2 + - + +
29B GLY* 4.3 1.7 + - - -
45B LYS* 3.5 45.2 + - + -
47B ILE* 4.2 28.9 - - + -
56B LEU* 4.1 10.3 - - + -
58B LEU* 3.7 22.2 - - + -
153B ASN* 4.8 4.6 + - - +
156B ALA* 3.9 9.8 - - + +
157B VAL* 3.8 32.9 - - + +
160B PHE* 3.3 50.7 - + + -
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Residues in contact with VAL 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 THR* 2.8 24.7 + - + +
24B ILE* 4.2 3.8 - - - +
26B PHE* 1.3 78.4 - - + +
28B GLU* 1.3 70.4 + - + +
43B PHE* 3.9 28.7 - - + -
44B THR 4.2 13.7 - - - +
45B LYS* 3.2 34.6 + - + +
58B LEU* 3.7 27.8 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 2.7 35.2 + - + +
27B VAL* 1.3 88.1 - - + +
29B GLY* 1.3 59.2 + - - +
30B GLN* 3.2 32.2 + - + +
43B PHE* 5.0 10.3 - - - -
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Residues in contact with GLY 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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24B ILE 3.3 0.4 + - - -
25B GLN* 2.8 40.6 + - - +
26B PHE 4.3 1.3 + - - -
27B VAL 3.7 1.2 - - - -
28B GLU* 1.3 73.3 - - - +
30B GLN* 1.3 58.0 + - - +
153B ASN* 3.9 9.0 + - - +
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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