Contacts of the strand formed by residues 29 - 35 (chain G) in PDB entry 3L3T
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 LYS 29 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G PHE* 3.7 12.9 - - - -
24G ASP* 3.2 27.5 + - - +
27G GLU* 3.7 29.2 - - + +
28G GLY* 1.3 79.7 - - - +
30G CYS* 1.3 72.0 + - - +
31G ALA* 4.9 2.6 - - - +
48G GLU* 6.0 1.1 - - - +
52G MET* 3.7 10.8 - - + -
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Residues in contact with CYS 30 (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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21G TRP* 4.3 11.4 - - + -
22G TYR 3.2 4.9 - - - +
23G PHE* 3.7 7.6 - - - -
29G LYS* 1.3 88.8 - - - +
31G ALA* 1.3 60.2 + - - +
48G GLU* 4.3 18.8 - - + +
51G CYS* 2.0 68.0 - - + -
52G MET* 3.2 22.0 - - + +
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Residues in contact with ALA 31 (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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21G TRP* 3.4 6.7 - - - -
22G TYR* 2.8 60.7 + - + +
24G ASP* 4.9 8.1 - - + +
27G GLU* 5.9 3.4 - - + -
29G LYS* 3.8 3.1 + - - +
30G CYS* 1.3 73.7 - - - +
32G PRO* 1.3 72.9 - - + +
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Residues in contact with PRO 32 (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 ARG 3.4 9.0 - - - +
21G TRP* 3.5 31.9 - - + -
22G TYR* 3.9 5.7 - - - -
30G CYS 4.8 0.2 - - - +
31G ALA* 1.3 92.7 - - + +
33G PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 33 (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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9G ALA* 4.1 16.8 - - + -
10G GLU 3.4 29.8 - - - -
11G THR* 4.9 2.0 - - + -
18G ILE 3.6 0.3 - - - +
19G SER* 3.9 0.5 - - - -
20G ARG* 2.8 47.4 + - + +
21G TRP 3.7 21.1 - - - -
22G TYR* 3.7 30.1 - + + -
32G PRO* 1.3 75.5 - - - +
34G PHE* 1.3 81.1 + - - +
35G TYR* 3.8 16.2 - - + -
43G ASN 4.1 4.5 - - - -
44G ASN* 3.8 27.8 - - + -
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Residues in contact with PHE 34 (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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151C TYR* 4.3 25.8 - + - +
192C GLN* 5.5 3.7 - - + +
11G THR* 3.5 23.7 - - - +
17G MET* 3.5 49.4 - - + -
18G ILE 3.6 8.7 - - - -
19G SER* 3.8 20.9 - - - -
33G PHE* 1.3 87.4 - - - +
35G TYR* 1.3 59.9 + - - +
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Residues in contact with TYR 35 (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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192C GLN* 5.3 0.7 - - - -
10G GLU 3.6 12.8 - - - -
11G THR* 3.3 15.9 - - - +
16G ALA 3.4 4.9 - - - +
17G MET* 3.7 0.2 - - - -
18G ILE* 2.9 46.6 + - + +
20G ARG* 4.0 22.7 - - + -
33G PHE* 3.8 12.1 + - + -
34G PHE* 1.3 73.2 - - - +
36G GLY* 1.3 60.8 + - - +
37G GLY* 3.6 23.0 + - - -
38G CYS* 3.1 29.5 + - - -
39G GLY 2.8 30.6 + - - -
40G GLY* 4.5 1.3 - - - -
44G ASN* 3.3 29.4 - - - +
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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