Contacts of the strand formed by residues 16 - 22 (chain C) in PDB entry 1T0R
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 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A PRO* 3.7 0.5 - - - +
395A THR* 3.0 42.6 + - + +
404A ILE* 3.6 29.6 - - + +
414A VAL* 3.4 11.4 - - + +
415A LYS 4.9 0.4 - - - -
416A ASP* 4.8 9.9 - - + +
7C MET* 3.5 22.7 - - + +
8C SER 3.1 14.4 - - - +
9C ASN* 3.0 41.7 - - + +
15C VAL* 1.3 87.1 - - - +
17C GLN* 1.3 63.0 + - - +
78C THR* 4.5 10.5 - - + +
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TYR* 5.4 1.2 - - - -
338A TRP* 3.8 15.1 - - + -
390A PRO* 5.6 1.2 - - - +
392A THR* 3.7 26.2 - - + +
393A LEU 3.8 4.3 - - - +
394A PRO* 4.7 5.8 - - + -
395A THR* 3.8 5.8 - - - +
7C MET* 3.4 1.9 - - - -
8C SER* 2.7 42.4 + - - +
13C ASP* 4.1 0.9 - - - +
15C VAL* 4.1 12.1 - - + +
16C ILE* 1.3 79.9 - - - +
18C LEU* 1.3 64.6 + - - +
19C VAL* 3.4 6.5 + - + +
34C CYS 5.1 0.2 - - - +
37C HIS* 3.2 24.5 + - - +
38C SER* 3.4 12.6 + - - -
41C ARG* 5.9 0.4 - - - +
42C ARG* 2.8 34.6 + - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A THR* 2.5 33.4 + - - +
393A LEU* 2.8 29.6 + - + +
394A PRO 5.1 0.7 - - - +
395A THR* 4.1 2.4 + - - +
451A VAL* 4.5 12.8 - - + -
454A PHE* 3.9 33.0 - - + -
455A LEU* 4.0 22.7 - - + -
5C PRO* 4.3 9.2 - - + -
6C ILE 4.0 3.8 - - - +
7C MET* 3.4 35.4 - - + -
17C GLN* 1.3 71.3 - - - +
19C VAL* 1.3 68.5 + - - +
20C PRO* 4.2 7.4 - - + +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.0 46.4 + - + +
8C SER* 3.5 26.2 - - - -
17C GLN* 3.7 7.9 - - + +
18C LEU* 1.3 83.3 - - - +
20C PRO* 1.3 74.4 - - + +
21C VAL* 4.6 2.9 - - + -
33C LYS* 3.7 31.4 - - + +
34C CYS* 4.0 11.7 - - - +
37C HIS* 4.0 20.2 - - + +
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Residues in contact with PRO 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A THR* 5.1 3.1 - - - +
3C THR* 5.0 12.3 - - + -
4C PHE 3.6 8.1 - - - +
5C PRO* 4.5 6.3 - - + -
18C LEU* 4.2 13.0 - - + +
19C VAL* 1.3 91.1 - - + +
21C VAL* 1.3 65.1 + - - +
33C LYS* 3.9 14.2 + - - +
37C HIS* 5.5 5.2 - - - +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR* 3.2 10.0 - - - +
4C PHE* 2.9 49.3 + - + +
6C ILE* 3.8 18.2 - - + -
19C VAL* 3.7 16.2 - - + +
20C PRO* 1.3 80.9 - - - +
22C ASP* 1.3 61.8 + - - +
25C ASP* 3.9 12.1 - - - +
30C VAL* 4.0 28.9 - - + +
33C LYS* 4.2 7.4 - - + +
68C VAL* 3.7 24.7 - - + -
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ALA* 3.2 26.2 + - - +
3C THR* 4.0 4.7 + - - +
21C VAL* 1.3 77.7 - - - +
23C THR* 1.3 66.3 + - - +
24C GLU* 2.9 33.5 + - - +
25C ASP* 2.9 37.5 + - - +
33C LYS* 4.2 6.1 - - - +
68C VAL* 3.1 15.0 - - - +
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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
------------------------------------------------------------
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