Contacts of the strand formed by residues 20 - 28 (chain H) in PDB entry 4KYI
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 CYS 20 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19H ILE* 1.3 76.2 - - - +
21H GLN* 1.3 61.7 + - - +
22H PHE* 3.1 37.5 - - + -
68H THR* 5.8 6.3 - - + -
69H THR 3.5 3.8 + - - +
70H VAL* 3.8 9.5 - - + -
71H LYS 3.3 12.9 + - - -
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Residues in contact with GLN 21 (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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466G ASP* 4.8 0.3 - - - +
468G SER* 3.9 11.3 + - - -
469G SER* 3.2 36.9 + - - -
472G ASN* 3.8 6.7 - - - +
473G TYR* 3.4 14.1 + - - -
19H ILE* 2.8 23.5 + - + +
20H CYS* 1.3 72.0 - - - +
22H PHE* 1.3 73.1 + - - +
71H LYS* 3.3 38.7 + - + +
73H GLU* 3.7 21.2 + - + +
95H GLN* 4.5 1.7 + - - +
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Residues in contact with PHE 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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20H CYS* 3.1 46.2 - - + -
21H GLN* 1.3 78.8 - - - +
23H LYS* 1.3 60.2 + - - +
70H VAL* 4.4 14.1 - - + -
71H LYS 2.7 13.5 + - - +
72H PHE* 3.4 16.9 - + + -
73H GLU* 2.5 37.4 + - - +
95H GLN* 3.3 31.2 - - + +
96H ALA* 5.7 1.3 - - + -
182H LEU* 3.7 50.9 - - + -
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Residues in contact with LYS 23 (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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476G GLN* 4.7 14.4 + - - +
22H PHE* 1.3 73.0 - - - +
24H LEU* 1.3 62.5 + - - +
73H GLU* 3.4 20.9 + - - +
75H TRP* 3.3 40.7 - - + +
89H MET 3.5 16.4 + - - -
90H TYR* 3.2 25.8 + - - +
93H GLY* 3.8 32.2 - - - +
94H ALA* 3.6 16.1 - - + +
95H GLN* 2.9 28.1 + - - +
96H ALA* 3.4 9.4 + - - +
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Residues in contact with LEU 24 (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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23H LYS* 1.3 77.6 - - - +
25H VAL* 1.3 75.0 + - - +
26H LEU* 4.0 13.7 - - + -
72H PHE* 4.1 31.4 - - + -
73H GLU 2.5 16.1 + - - +
74H ILE* 4.3 10.3 - - + -
75H TRP* 2.7 35.2 + - - +
96H ALA* 3.5 24.9 - - + +
98H ILE* 3.9 30.1 - - + -
175H PHE* 4.2 24.2 - - + -
178H ILE* 4.5 8.3 - - + -
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Residues in contact with VAL 25 (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 LEU* 1.3 79.5 - - - +
26H LEU* 1.3 67.5 + - - +
27H LEU* 4.1 13.6 - - + +
75H TRP* 3.6 6.7 - - + +
77H THR* 3.6 26.9 - - + -
90H TYR* 3.9 24.2 - - + +
91H TYR* 4.1 24.5 - - + +
94H ALA* 4.4 3.1 - - + -
96H ALA 3.3 14.4 + - - +
97H ALA* 3.3 13.1 - - + +
98H ILE 2.8 25.8 + - - +
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Residues in contact with LEU 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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24H LEU* 4.0 10.5 - - + -
25H VAL* 1.3 74.1 - - - +
27H LEU* 1.3 53.9 + - - +
34H LYS* 3.8 40.7 - - + +
37H LEU* 4.7 7.6 - - + -
38H VAL* 3.8 15.0 - - + -
74H ILE* 3.6 31.0 - - + -
75H TRP 3.2 17.6 + - - +
76H ASP* 4.3 5.6 - - - +
77H THR* 2.2 37.1 + - - +
98H ILE* 3.3 24.5 - - + +
100H VAL* 4.6 8.1 - - + -
175H PHE* 4.6 7.0 - - + -
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Residues in contact with LEU 27 (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 VAL* 4.1 22.2 - - + -
26H LEU* 1.3 83.9 - - - +
28H GLY* 1.3 53.5 + - - +
34H LYS* 3.8 4.9 - - - -
77H THR* 3.8 13.9 - - + +
87H ALA* 5.0 8.5 - - + -
90H TYR* 5.8 0.4 - - + -
91H TYR* 4.6 9.0 - - + -
97H ALA* 5.1 1.1 - - + -
98H ILE 2.8 12.7 + - - +
99H VAL* 3.2 7.4 - - + +
100H VAL* 2.7 34.7 + - - +
115H TRP* 3.9 45.8 - - + -
119H LEU* 3.7 39.9 - - + -
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Residues in contact with GLY 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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27H LEU* 1.3 76.5 - - - +
29H GLU* 1.3 68.5 + - - +
32H VAL* 4.7 0.4 - - - -
34H LYS* 3.7 9.5 + - - +
77H THR* 5.0 0.4 + - - -
79H GLY* 3.1 22.3 - - - +
99H VAL* 5.1 1.3 - - - -
100H VAL 3.5 14.8 - - - -
108H THR 6.1 0.2 - - - -
112H ALA* 5.9 0.9 - - - -
115H TRP* 4.1 24.1 + - - +
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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