Contacts of the strand formed by residues 18 - 23 (chain H) in PDB entry 4ZZ7
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 ARG 18 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN* 3.8 0.8 - - - +
17H THR* 1.3 88.1 + - - +
19H SER* 1.3 64.6 + - - +
35H ASP* 3.2 9.9 + - - +
36H LEU* 2.8 45.6 + - + +
37H ALA 4.3 7.9 + - - -
38H SER* 5.0 4.0 - - - +
204H ASP* 2.8 40.1 + - - -
206H GLU* 2.9 37.3 + - - +
18K ARG* 3.1 15.5 - - + +
19K SER 3.5 13.7 - - - +
20K GLN* 3.0 29.8 + - + -
21K ASN* 5.0 1.1 + - - -
36K LEU* 3.4 16.2 - - + -
204K ASP* 3.9 6.7 + - - +
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Residues in contact with SER 19 (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 THR* 5.8 3.1 - - - -
18H ARG* 1.3 76.7 - - - +
20H GLN* 1.3 60.1 + - - +
33H GLN* 3.4 23.5 + - - -
34H LEU 3.1 15.9 - - - -
35H ASP* 4.5 2.7 - - - -
36H LEU* 4.2 3.1 - - - -
18K ARG* 3.5 4.7 - - - +
19K SER* 2.7 52.8 + - - +
21K ASN* 5.7 0.3 + - - -
33K GLN* 4.4 5.2 + - - -
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Residues in contact with GLN 20 (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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19H SER* 1.3 78.1 - - - +
21H ASN* 1.3 79.7 + - - +
22H VAL 3.4 0.5 + - - -
33H GLN* 3.5 4.6 - - - -
34H LEU* 2.7 45.0 + - + +
36H LEU* 3.7 15.8 - - + +
175H GLU* 3.4 44.8 + - + +
176H ARG* 4.9 7.9 - - - +
204H ASP* 5.2 0.5 - - - +
17K THR* 3.3 19.3 + - - +
18K ARG* 3.3 26.2 - - - +
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 1.3 88.6 + - - +
22H VAL* 1.3 60.3 + - - +
23H PHE* 4.0 23.0 - - + -
30H ILE* 3.6 31.1 - - + +
32H LYS 3.8 4.5 - - - -
33H GLN* 2.6 32.2 + - - +
175H GLU 5.2 0.5 - - - +
176H ARG* 5.9 0.7 - - - -
16K ASN* 2.6 36.6 + - - +
17K THR* 4.4 5.5 + - - +
18K ARG 4.6 2.3 - - - +
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ILE* 4.5 2.9 - - + -
20H GLN* 4.0 1.6 - - + +
21H ASN* 1.3 76.7 - - - +
23H PHE* 1.3 66.3 + - - +
30H ILE* 3.9 2.8 - - - -
31H GLY* 3.0 20.5 + - - -
32H LYS* 3.0 41.1 + - + +
34H LEU* 3.8 29.2 - - + +
89H GLU* 3.9 16.4 - - + +
175H GLU 3.8 14.8 - - - +
176H ARG* 4.3 15.0 - - - +
178H PRO* 4.2 10.3 - - + -
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Residues in contact with PHE 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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21H ASN* 4.0 19.5 - - + -
22H VAL* 1.3 82.5 - - - +
24H ASN* 1.3 61.4 + - - +
25H PRO* 3.6 9.8 - - + +
28H GLY 3.4 25.8 - - - -
29H GLU 3.6 8.1 - - - +
30H ILE* 3.6 24.5 - - + -
31H GLY* 4.5 2.7 - - - -
88H GLU* 3.9 0.3 - - - +
89H GLU* 3.9 19.4 - - - +
176H ARG 4.9 3.5 + - - +
324H ILE 5.3 2.5 - - - +
325H THR* 5.7 8.3 - - + -
362H PHE* 4.2 27.8 - + + -
16K ASN* 4.1 17.5 - - + -
17K THR* 4.8 13.9 - - + -
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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