Contacts of the strand formed by residues 21 - 30 (chain H) in PDB entry 1S7X
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 ASN 21 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11H SER* 3.8 5.7 - - - -
13H HIS* 2.9 59.5 + - - +
14H PRO 3.7 10.1 + - - -
15H PRO* 3.7 12.1 - - - +
16H GLU 4.7 2.2 - - - +
19H LYS* 3.9 8.4 + - - +
20H PRO* 1.3 76.1 - - - +
22H ILE* 1.3 83.4 + - - +
69H GLU* 3.7 4.5 - - - +
70H PHE* 2.8 48.0 + - + +
72H PRO* 4.3 3.9 - - + +
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H SER* 3.3 4.2 - - - -
12H ARG* 2.8 77.7 + - + +
13H HIS* 5.1 2.6 - - + +
21H ASN* 1.3 89.3 + - - +
23H LEU* 1.3 61.2 + - - +
24H ASN* 3.9 6.5 + - - +
67H HIS* 3.6 35.4 - - + +
68H THR 3.5 12.6 - - - +
69H GLU* 4.7 13.5 - - + -
70H PHE* 3.7 3.8 - - - -
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.2 16.2 - - + -
10H TYR 3.7 16.4 - - - +
22H ILE* 1.3 71.7 - - - +
24H ASN* 1.3 63.5 + - - +
39H MET* 4.1 10.7 - - + +
46H ILE* 5.8 0.2 - - + -
67H HIS* 3.1 5.5 - - - +
68H THR* 3.0 43.5 + - + +
70H PHE* 3.4 34.5 - - + -
78H TYR* 3.4 40.6 - - + -
79H ALA 5.0 4.5 - - - +
95H TRP* 3.8 26.7 - - + -
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Residues in contact with ASN 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G PRO 3.6 0.4 + - - -
236G ALA 2.8 31.3 + - - +
237G GLY* 4.9 1.0 - - - -
8H GLN 4.3 0.4 - - - -
9H VAL* 3.3 10.0 - - - +
10H TYR* 2.8 68.0 + - + +
12H ARG* 4.0 13.8 + - - +
22H ILE* 4.1 5.1 - - - +
23H LEU* 1.3 76.7 - - - +
25H CYS* 1.3 60.3 + - - +
26H TYR 4.1 0.4 - - - -
39H MET* 4.7 1.3 - - - -
65H LEU* 3.9 18.8 - - + +
66H ALA 3.3 2.0 - - - -
67H HIS* 3.1 22.9 - - - +
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Residues in contact with CYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ILE* 3.9 11.7 - - - -
8H GLN 3.4 4.3 - - - -
9H VAL* 4.6 1.8 - - + +
23H LEU 4.3 0.2 + - - -
24H ASN* 1.3 72.8 - - - +
26H TYR* 1.3 61.0 + - - +
27H VAL* 3.9 19.6 + - - +
37H ILE* 4.4 1.1 - - - -
39H MET* 4.1 12.1 - - - -
64H ILE 3.9 0.5 - - - +
65H LEU* 3.7 2.4 - - - -
66H ALA* 2.7 43.8 + - + +
80H CYS* 2.0 54.3 - - + -
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Residues in contact with TYR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G GLU* 5.9 2.5 - - + -
233G THR 3.8 16.8 + - - -
234G ARG* 4.2 8.7 - - + -
235G PRO* 3.4 42.2 - - + +
241G PHE* 5.8 1.6 - - - -
6H GLN 3.6 1.2 - - - +
7H ILE* 3.4 3.6 - - - -
8H GLN* 2.9 42.6 + - + +
10H TYR* 3.5 22.4 - - + +
24H ASN 4.1 0.2 - - - -
25H CYS* 1.3 71.6 - - - +
27H VAL* 1.3 59.5 + - - +
28H THR* 3.3 32.9 + - + +
63H TYR* 4.2 26.2 - + - -
64H ILE 3.7 12.1 - - - -
65H LEU* 4.0 9.4 - - + -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO* 3.3 33.4 - - + -
6H GLN 3.3 5.4 - - - +
7H ILE* 4.2 5.8 - - + -
25H CYS* 3.9 22.4 - - - +
26H TYR* 1.3 75.2 - - - +
28H THR* 1.3 61.7 + - - +
30H PHE* 3.4 16.3 - - + -
35H ILE* 3.9 9.6 - - + -
37H ILE* 3.5 24.5 - - + -
63H TYR* 3.2 3.5 - - - +
64H ILE* 2.8 41.0 + - + +
82H VAL* 4.2 10.3 - - + -
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G GLU* 6.0 3.0 - - + +
5H PRO* 3.4 4.2 - - - +
6H GLN* 2.9 46.2 + - - +
26H TYR* 3.3 48.2 - - + +
27H VAL* 1.3 78.1 - - - +
29H GLN* 1.3 74.9 + - - +
30H PHE* 3.4 3.8 - - - -
62H PHE 3.5 6.7 - - - -
63H TYR* 3.9 7.6 - - + -
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G GLU* 5.9 3.3 - - - +
3H LYS* 3.4 18.2 - - + +
4H THR 3.4 12.7 - - - +
6H GLN* 4.0 18.3 - - + +
28H THR* 1.3 90.5 + - - +
30H PHE* 1.3 58.4 + - - +
57H SER* 5.8 1.4 + - - -
59H ASP* 2.8 28.7 + - - -
61H SER* 3.4 27.1 + - - +
62H PHE 3.0 6.9 + - - -
63H TYR* 4.9 0.2 - - - +
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Residues in contact with PHE 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H LYS* 3.4 12.3 - - - +
5H PRO* 3.9 14.8 - - + -
27H VAL* 3.4 41.1 - - + -
28H THR 3.8 5.4 - - - -
29H GLN* 1.3 78.1 - - - +
31H HIS* 1.3 64.5 + - - +
32H PRO 3.6 13.0 - - - -
33H PRO* 3.5 23.6 - - + -
35H ILE* 3.8 22.7 - - + -
61H SER* 3.9 3.2 - - - -
62H PHE* 3.1 67.7 + - + -
63H TYR* 3.8 8.3 - - - -
64H ILE* 4.3 7.0 - - + -
84H HIS* 3.7 11.9 - + - +
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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