Contacts of the strand formed by residues 28 - 36 (chain I) in PDB entry 4TPI
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 28 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I TYR* 4.1 19.0 + - - -
24I ASN 3.0 8.6 + - - -
25I ALA 3.2 11.3 + - - -
27I ALA* 1.3 79.6 - - - +
29I LEU* 1.3 63.1 + - - +
52I MET* 5.5 3.5 - - - +
57I GLY 5.7 0.5 + - - -
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 4.3 5.8 - - - -
24I ASN* 3.0 34.2 + - - +
27I ALA* 3.1 34.2 - - + +
28I GLY* 1.3 82.1 - - - +
30I CYS* 1.3 66.6 + - - +
31I GLN* 3.8 19.1 - - + +
52I MET* 4.8 10.8 - - + -
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Residues in contact with CYS 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TYR* 4.4 13.9 - - + -
22I PHE 3.2 4.0 - - - -
23I TYR* 3.8 13.5 - - - -
29I LEU* 1.3 81.5 - - - +
31I GLN* 1.3 62.0 + - - +
48I ALA* 4.7 5.0 - - + +
51I CYS* 2.0 62.8 - - + -
52I MET* 3.5 24.8 - - + -
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Residues in contact with GLN 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TYR* 3.1 11.0 - - - -
22I PHE* 2.8 53.9 + - + -
24I ASN* 2.8 43.5 + - + -
27I ALA* 4.1 3.0 - - - +
29I LEU* 3.7 18.0 - - + +
30I CYS* 1.3 79.0 + - - +
32I THR* 1.3 64.1 + - - +
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Residues in contact with THR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ILE* 3.8 20.0 - - + -
20I ARG 3.0 9.2 - - - +
21I TYR* 3.5 34.5 - - + +
22I PHE* 3.7 7.4 - - - -
31I GLN* 1.3 81.5 + - - +
33I PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I PRO* 3.6 22.0 - - + -
10I TYR 3.3 26.2 - - - -
11I THR* 4.5 4.0 - - - -
19I ILE* 3.6 6.4 - - - +
20I ARG* 2.9 48.4 + - + +
21I TYR 3.7 21.1 - - - -
22I PHE* 3.6 25.8 - + + -
32I THR* 1.3 74.4 - - - +
34I VAL* 1.3 87.0 + - - +
35I TYR* 3.7 6.2 + - + -
43I ASN 3.9 11.7 - - - -
44I ASN* 3.6 25.4 - - + -
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Residues in contact with VAL 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I THR* 2.7 27.9 + - + +
16I ALA 4.3 5.2 - - - +
17I ARG* 3.8 47.3 - - + -
18I ILE 3.8 2.2 - - - +
19I ILE* 5.2 6.3 - - + -
33I PHE* 1.3 82.8 - - - +
35I TYR* 1.3 61.1 + - - +
151Z TYR* 3.9 19.1 - - + +
192Z GLN* 4.3 10.1 - - + -
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Residues in contact with TYR 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I TYR 3.8 9.0 - - - -
11I THR* 3.7 7.0 - - - -
16I ALA 3.7 2.1 - - - +
18I ILE* 2.7 52.1 + - + +
20I ARG* 3.7 48.2 - - + -
33I PHE* 3.7 8.2 + - + -
34I VAL* 1.3 73.6 - - - +
36I GLY* 1.3 62.2 - - - +
37I GLY* 3.3 21.9 + - - -
38I CYS* 3.0 48.3 - - - -
39I ARG 3.4 0.5 + - - -
40I ALA* 3.1 33.1 + - + +
44I ASN* 3.4 11.2 - - - -
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Residues in contact with GLY 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I THR* 2.9 26.9 + - - +
14I CYS* 3.0 34.1 - - - +
16I ALA* 2.8 36.2 + - - +
35I TYR* 1.3 70.8 - - - +
37I GLY* 1.3 58.2 + - - +
38I CYS 3.5 2.7 - - - -
57Z HIS* 3.5 0.5 - - - -
192Z GLN* 4.3 0.2 - - - -
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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