Contacts of the strand formed by residues 62 - 70 (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 PHE 62 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G THR* 4.0 11.2 - - + -
94G THR* 4.2 2.9 - - + -
96G GLN* 3.4 30.7 - - - -
29H GLN 3.0 23.3 + - - -
30H PHE* 3.1 50.7 + - + +
31H HIS* 4.0 13.5 - - - -
33H PRO* 3.7 44.9 - - + -
54H MET* 3.8 24.9 - - + -
55H SER 3.3 17.9 - - - +
56H PHE* 3.8 15.5 - + + -
60H TRP 3.8 5.8 - - - -
61H SER* 1.3 73.0 - - - +
63H TYR* 1.3 62.2 + - - +
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Residues in contact with TYR 63 (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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27G TYR* 4.3 12.8 + - - -
26H TYR* 4.2 21.5 - + + -
27H VAL 3.2 11.9 - - - +
28H THR* 3.9 18.4 - - + -
29H GLN 4.9 0.2 - - - +
30H PHE* 3.8 3.4 - - - -
53H ASP 4.4 0.5 - - - +
54H MET* 4.4 1.0 - - - -
55H SER* 3.0 55.9 + - - +
56H PHE 3.6 19.3 + - - -
57H SER* 3.2 31.6 - - - +
62H PHE* 1.3 75.5 - - - +
64H ILE* 1.3 70.5 + - - +
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Residues in contact with ILE 64 (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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25H CYS 3.9 0.7 - - - +
26H TYR* 3.7 5.9 - - - -
27H VAL* 2.8 38.1 + - + +
30H PHE* 4.4 11.9 - - + -
35H ILE* 4.7 13.7 - - + -
37H ILE* 3.2 32.3 - - + -
51H MET* 4.2 18.2 - - + -
52H SER* 3.6 28.9 - - - +
53H ASP 4.2 4.3 - - - +
54H MET* 4.6 14.8 - - + +
63H TYR* 1.3 82.4 - - - +
65H LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 65 (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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235G PRO* 4.1 15.3 - - + +
237G GLY* 4.1 26.9 - - - +
10H TYR* 4.0 12.8 - - - +
24H ASN* 3.9 24.7 - - + +
25H CYS 3.7 9.4 - - - +
26H TYR* 4.0 15.9 - - + -
50H GLU 4.1 0.3 - - - +
51H MET* 3.8 3.8 - - - +
52H SER* 2.9 44.5 + - - +
63H TYR* 5.7 0.4 - - - -
64H ILE* 1.3 72.8 - - - +
66H ALA* 1.3 72.6 + - - +
67H HIS* 5.0 10.2 + - + +
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Residues in contact with ALA 66 (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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24H ASN* 3.3 1.4 - - - -
25H CYS* 2.7 43.9 + - + +
37H ILE* 4.0 20.2 - - + -
39H MET* 3.8 12.3 - - + -
49H VAL* 4.3 0.4 - - + -
50H GLU 3.3 6.5 - - - +
51H MET* 3.6 25.1 - - + -
64H ILE 4.2 0.2 - - - -
65H LEU* 1.3 77.1 - - - +
67H HIS* 1.3 62.0 + - - +
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Residues in contact with HIS 67 (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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237G GLY* 6.2 1.1 - - - -
12H ARG* 4.6 11.9 + - - -
22H ILE* 3.6 27.9 - - + +
23H LEU 3.1 9.9 - - - +
24H ASN* 3.1 28.0 - - - +
39H MET* 3.1 11.2 - - - +
50H GLU* 2.8 66.9 + - + +
51H MET 6.2 0.4 - - - -
52H SER 5.9 0.6 + - - -
65H LEU* 5.0 11.6 + - + +
66H ALA* 1.3 73.6 - - - +
68H THR* 1.3 62.5 + - - +
69H GLU* 6.5 0.2 - - + -
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Residues in contact with THR 68 (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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22H ILE* 3.5 7.3 - - - -
23H LEU* 3.0 40.7 + - + +
39H MET* 3.5 23.1 - - + -
46H ILE* 3.5 30.3 - - + +
48H LYS 2.9 23.1 + - - -
49H VAL* 4.1 3.6 - - - -
50H GLU* 5.8 1.6 - - - -
67H HIS* 1.3 79.7 - - - +
69H GLU* 1.3 73.6 + - - +
70H PHE* 5.0 1.6 - - + -
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Residues in contact with GLU 69 (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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21H ASN 3.7 9.9 - - - +
22H ILE* 4.6 12.1 - - + +
46H ILE* 5.4 1.7 - - - +
48H LYS* 4.9 11.5 + - - -
67H HIS* 6.5 0.2 - - + -
68H THR* 1.3 86.6 + - - +
70H PHE* 1.3 66.7 + - - +
78H TYR* 5.7 0.3 - - - -
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Residues in contact with PHE 70 (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* 4.1 4.0 - - - -
20H PRO* 3.7 0.3 - - - +
21H ASN* 2.8 61.6 + - + +
22H ILE 3.7 6.3 - - - -
23H LEU* 3.4 51.8 - - + -
68H THR* 5.0 1.3 - - + -
69H GLU* 1.3 77.9 - - - +
71H THR* 1.3 62.4 + - - +
72H PRO* 3.7 20.0 - - + +
78H TYR* 3.5 44.0 - + + +
95H TRP* 3.6 38.4 - + - -
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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