Contacts of the strand formed by residues 21 - 26 (chain D) in PDB entry 1TH7
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 LEU 21 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASN* 1.3 77.0 - - - +
22D VAL* 1.3 65.7 + - - +
33D ARG* 4.0 21.1 - - - +
34D GLY* 3.5 31.6 - - - +
35D MET* 3.7 15.5 - - + +
77D PRO* 3.7 2.1 - - - +
78D LEU* 2.9 57.4 + - + -
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D SER* 3.9 26.5 - - - +
20D ASN 3.9 7.9 - - - +
21D LEU* 1.3 82.0 - - - +
23D LEU* 1.3 59.8 + - - +
24D VAL* 4.1 11.7 - - + -
32D VAL 4.1 0.2 - - - +
33D ARG* 3.2 6.2 - - - +
34D GLY 2.9 39.3 + - - +
36D LEU* 4.1 13.9 - - + -
47D LEU* 3.7 24.7 - - + -
75D ILE* 4.5 11.2 - - + -
76D SER 3.3 10.8 - - - +
77D PRO* 4.1 8.1 - - + -
78D LEU* 3.9 7.2 - - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 1.3 73.6 - - - +
24D VAL* 1.3 65.5 + - - +
25D LYS* 4.1 1.3 + - + +
31D GLU* 4.0 27.4 - - + +
32D VAL 3.6 20.2 - - - +
33D ARG* 4.2 9.6 - - + -
53D ILE* 4.3 13.9 - - + -
74D LEU 4.0 0.9 - - - +
75D ILE* 3.6 3.1 - - - +
76D SER* 2.8 40.0 + - - +
78D LEU* 3.8 25.5 - - + +
60E LYS* 6.1 2.7 - - - +
62E LEU* 6.0 6.3 - - + -
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 4.1 12.8 - - + -
23D LEU* 1.3 79.9 - - - +
25D LYS* 1.3 64.7 + - - +
26D LEU* 3.7 25.0 + - + +
31D GLU* 3.4 4.3 - - - -
32D VAL* 2.7 43.9 + - + +
45D LEU* 3.9 31.9 - - + -
47D LEU* 4.0 21.8 - - + -
67D ILE* 4.6 1.6 - - + -
72D VAL* 4.1 8.1 - - + -
74D LEU 3.5 9.6 - - - +
75D ILE* 4.5 6.3 - - + -
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.1 2.1 - - + +
24D VAL* 1.3 72.4 - - - +
26D LEU* 1.3 75.5 + - - +
29D ASN* 3.5 36.1 + - - +
30D LYS 3.3 12.1 - - - +
31D GLU* 3.6 21.1 - - + +
72D VAL* 3.8 3.3 - - - -
73D ILE* 2.8 37.2 + - + -
74D LEU* 2.9 28.8 + - + +
28E GLY 3.5 15.2 + - - -
29E ASN* 2.7 37.4 + - - +
30E LYS* 5.9 1.0 - - - +
52E GLU* 5.3 1.0 + - - -
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ILE* 4.3 20.4 - - + -
74C LEU* 4.9 7.6 - - + -
24D VAL* 3.8 27.6 - - + +
25D LYS* 1.3 92.7 - - - +
27D LYS* 1.3 71.7 + - - +
29D ASN 3.6 0.2 + - - -
30D LYS* 2.8 32.0 + - + +
32D VAL* 4.4 24.9 - - + -
67D ILE* 3.9 22.7 - - + -
71D ASN* 3.2 20.4 - - + +
72D VAL* 4.1 4.5 - - + -
73D ILE* 3.6 5.9 - - - +
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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