Contacts of the strand formed by residues 17 - 22 (chain G) in PDB entry 1D3B
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 17 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G HIS* 1.3 75.8 - - - +
18G VAL* 1.3 65.4 + - - +
29G ARG* 3.4 44.4 - - + +
30G GLY* 3.2 20.0 - - - +
31G LYS* 4.4 7.9 - - + +
72G ILE 4.6 0.3 - - - +
73G LEU 5.2 0.2 - - - -
74G PRO* 4.0 14.4 - - - +
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Residues in contact with VAL 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA* 3.9 18.2 - - + -
16G HIS 3.6 6.5 + - - +
17G ILE* 1.3 80.8 - - - +
19G THR* 1.3 64.3 + - - +
29G ARG* 3.4 5.2 - - - +
30G GLY 2.7 31.8 + - - +
32G LEU* 3.9 23.6 - - + -
43G MET* 3.7 20.0 - - + +
71G LEU* 4.2 17.0 - - + -
72G ILE 3.5 9.6 - - - +
73G LEU* 3.7 25.8 - - + -
74G PRO* 4.1 3.1 - - + -
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Residues in contact with THR 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G VAL* 1.3 73.8 - - - +
20G CYS* 1.3 66.1 + - - +
21G GLU* 4.8 1.8 - - + +
27G VAL* 3.5 30.1 - - + -
28G TYR 3.5 3.6 - - - +
29G ARG* 3.6 28.3 + - + +
70G PHE* 4.0 3.7 - - + +
71G LEU* 3.1 7.2 - - - +
72G ILE* 2.7 64.1 + - + +
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Residues in contact with CYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G VAL 4.0 0.2 - - - -
19G THR* 1.3 77.3 - - - +
21G GLU* 1.3 62.0 + - - +
22G THR* 4.0 2.4 + - - -
26G GLU 3.8 0.9 - - - +
27G VAL* 3.5 1.4 - - - -
28G TYR* 2.7 46.9 + - + +
41G CYS* 6.0 0.4 - - - -
43G MET* 4.1 16.6 - - - -
63G ILE* 3.6 20.0 - - - -
68G ILE* 3.4 43.1 - - - -
70G PHE 3.7 3.1 - - - -
71G LEU* 4.1 11.7 - - + -
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Residues in contact with GLU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G THR* 4.1 2.3 - - + +
20G CYS* 1.3 73.5 - - - +
22G THR* 1.3 65.3 + - - +
25G GLY* 4.8 2.2 - - - -
26G GLU 3.5 9.4 - - - +
27G VAL* 3.6 21.0 - - + +
68G ILE* 3.6 1.9 - - - +
69G ARG* 2.6 55.0 + - - +
70G PHE* 2.9 40.5 + - + +
701G CIT 4.5 7.7 - - - -
25H ARG* 3.9 0.5 + - - -
65H ARG* 2.7 47.1 + - - -
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Residues in contact with THR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G CYS* 4.8 1.8 - - - +
21G GLU* 1.3 75.8 - - - +
23G ASN* 1.3 63.2 + - - +
24G THR 3.3 2.3 + - - -
25G GLY* 3.1 11.6 + - - -
26G GLU* 2.6 48.7 + - - +
28G TYR* 4.0 22.2 - - + -
63G ILE* 4.5 12.8 - - + -
67G LYS 3.1 14.1 - - - +
68G ILE* 4.2 0.4 - - - +
69G ARG* 3.5 16.2 + - - -
22L GLN* 3.5 26.7 - - - +
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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