Contacts of the strand formed by residues 30 - 37 (chain K) in PDB entry 5HJD
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 HIS 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17K ALA 5.1 2.5 - - - -
18K GLN* 3.3 14.4 - - - +
19K VAL* 3.3 26.6 - - + +
20K ARG* 4.3 0.9 - - - -
29K THR* 1.3 110.1 + - - +
31K ASP* 1.3 73.0 + - - +
32K TRP* 4.2 1.3 - - + -
76K SER* 3.2 3.1 - - - -
77K GLY 2.9 30.7 + - - +
78K TYR 4.7 4.2 + - - -
106K LEU* 3.5 45.9 - - + +
107K HIS 2.7 28.0 + - - -
108K LEU* 5.3 5.8 - - + -
109K GLU 5.8 0.4 - - - -
16M PRO* 5.6 7.9 - - + -
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Residues in contact with ASP 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG 4.6 0.3 - - - -
17K ALA* 3.6 0.5 - - - -
18K GLN* 2.8 39.2 + - + +
20K ARG* 3.0 42.3 + - + +
30K HIS* 1.3 77.3 - - - +
32K TRP* 1.3 61.1 + - - +
75K GLU 3.6 4.0 - - - +
76K SER* 2.9 22.7 + - - -
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Residues in contact with TRP 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 5.2 0.4 - - + -
16K ARG 3.1 14.4 - - - +
17K ALA* 4.1 10.5 - - + -
30K HIS* 4.9 1.6 - - + -
31K ASP* 1.3 77.8 - - - +
33K MET* 1.3 68.5 + - - +
34K VAL* 3.8 12.1 - - + -
55K LEU* 3.7 24.0 - - + -
59K PHE* 3.8 24.1 - + - -
73K VAL* 3.7 24.7 - - + -
74K GLU* 3.6 2.6 - - - +
75K GLU* 2.9 62.4 + - + +
77K GLY* 4.2 21.5 - - - +
79K ALA 5.0 2.2 + - - -
81K PHE* 4.0 14.1 - + - -
83K LEU* 4.7 0.2 - - + -
104K LEU* 3.6 33.0 - - + +
106K LEU* 4.1 16.6 - - + -
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Residues in contact with MET 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 3.1 5.5 - - - +
16K ARG* 2.8 87.2 + - + +
32K TRP* 1.3 76.5 - - - +
34K VAL* 1.3 68.1 + - - +
35K PHE* 3.6 31.0 - - + -
72K LYS* 3.6 30.7 - - + +
73K VAL 3.2 5.4 - - - +
74K GLU* 3.8 18.6 - - + +
202K SO4 3.9 13.0 - - - +
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Residues in contact with VAL 34 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K GLY 3.5 11.4 - - - +
15K HIS* 3.9 2.7 - - + -
32K TRP* 3.8 11.4 - - + -
33K MET* 1.3 76.5 - - - +
35K PHE* 1.3 65.3 + - - +
53K PHE* 4.0 13.8 - - + -
72K LYS* 3.4 3.8 - - - -
73K VAL* 2.9 55.3 + - + -
83K LEU* 4.1 10.3 - - + -
85K ILE* 4.4 16.6 - - + -
102K TYR* 4.2 14.8 - - + -
104K LEU* 3.7 24.0 - - + -
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Residues in contact with PHE 35 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12K GLU 4.4 0.7 - - - -
13K LEU* 3.7 4.7 - - - +
14K GLY* 2.8 71.7 + - - +
15K HIS* 3.8 5.2 - - - -
16K ARG* 6.0 1.3 - - - -
33K MET* 3.6 26.7 - - + -
34K VAL* 1.3 78.5 - - - +
36K VAL* 1.3 71.3 + - - +
37K ARG* 3.6 50.3 - - + -
53K PHE* 4.4 2.2 - - - -
71K TYR 3.2 10.3 - - - +
72K LYS* 4.7 0.7 - - - -
85K ILE* 5.2 0.2 - - - +
115K ASN* 5.8 3.4 - - - -
116K HIS 4.7 1.8 - - - -
117K LEU* 3.9 15.5 - - + -
202K SO4 3.6 26.5 - - - +
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Residues in contact with VAL 36 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K LEU* 4.7 10.3 - - + -
12K GLU 3.4 8.1 - - - +
13K LEU* 3.6 25.4 - - + -
35K PHE* 1.3 80.7 - - - +
37K ARG* 1.3 68.5 + - - +
44K ILE* 4.5 8.5 - - + -
51K VAL* 4.0 10.1 - - + -
53K PHE* 3.8 19.5 - - + -
71K TYR* 3.0 42.4 + - + +
85K ILE* 3.9 11.7 - - + -
87K VAL* 4.3 19.1 - - + -
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Residues in contact with ARG 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LEU* 3.6 10.2 - - - +
12K GLU* 2.6 60.1 + - + +
35K PHE* 3.6 31.4 - - + -
36K VAL* 1.3 76.3 - - - +
38K GLY* 1.3 66.3 + - - +
44K ILE* 3.7 12.3 - - - -
71K TYR* 5.1 0.4 - - - -
117K LEU* 3.7 13.5 - - - +
202K SO4 3.5 28.9 + - - +
116T HIS* 4.0 22.4 + - - +
117T LEU* 2.9 31.1 + - - +
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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