Contacts of the strand formed by residues 30 - 35 (chain K) in PDB entry 6R90
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 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19K VAL 4.1 0.2 - - - +
20K THR* 3.3 7.4 - - - +
21K GLY 2.9 32.7 + - - +
22K HIS* 3.4 2.6 - - - -
23K PHE* 2.4 42.8 + - + +
24K THR* 2.6 44.2 + - - +
25K SER 4.1 0.2 + - - -
28K ASP* 3.9 8.1 - - - +
29K LEU* 1.3 78.9 + - - +
31K LEU* 1.3 60.9 + - - +
32K LEU* 4.2 9.7 - - + +
41K ILE* 4.9 3.0 - - + +
42K TYR 3.5 8.9 + - - +
43K VAL* 4.3 9.5 - - - +
44K VAL* 4.5 2.7 - - - -
66K LEU* 5.4 0.2 - - + -
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Residues in contact with LEU 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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18K CYS* 4.4 2.5 - - + -
19K VAL 3.0 29.8 - - - +
20K THR* 3.9 5.6 - - + -
29K LEU 4.3 0.4 + - - -
30K ASN* 1.3 71.3 - - - +
32K LEU* 1.3 72.5 + - - +
33K ILE* 3.9 20.6 - - + -
40K GLU 3.8 0.9 - - - +
41K ILE* 3.4 4.3 - - - -
42K TYR* 2.9 42.1 + - + +
44K VAL* 4.4 12.5 - - + +
49K LEU* 4.0 18.8 - - + -
315K THR* 3.7 20.4 - - - +
317K LEU* 4.3 5.4 - - + -
323K PHE* 3.7 33.9 - - + -
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Residues in contact with LEU 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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18K CYS* 3.2 3.5 - - - -
19K VAL* 2.9 44.0 + - + +
23K PHE* 4.4 11.7 - - + -
30K ASN* 4.2 13.7 - - + -
31K LEU* 1.3 84.1 - - - +
33K ILE* 1.3 61.2 + - - +
39K LEU* 4.0 9.4 - - + -
40K GLU 3.4 2.2 - - - -
41K ILE* 4.0 28.7 - - + -
64K MET* 3.4 10.7 - - + +
66K LEU* 4.3 19.5 - - + -
77K LEU* 3.6 42.2 - - + -
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Residues in contact with ILE 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 VAL* 3.8 29.2 - - + -
17K GLY 3.4 10.8 - - - +
18K CYS* 4.7 0.7 - - + -
31K LEU* 3.9 20.6 - - + -
32K LEU* 1.3 79.2 - - - +
34K ALA* 1.3 64.1 + - - +
35K LYS* 4.1 10.9 + - + -
38K ARG 3.7 1.0 - - - +
39K LEU* 3.4 8.2 - - - +
40K GLU* 2.9 45.4 + - + +
42K TYR* 3.8 24.9 - - + -
49K LEU* 5.1 1.3 - - + -
64K MET* 4.1 0.4 - - - -
323K PHE* 3.3 35.0 - - + -
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Residues in contact with ALA 34 (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 VAL* 3.6 2.1 - - - -
16K ASN* 2.6 38.7 + - + -
17K GLY* 2.8 22.4 + - - +
33K ILE* 1.3 71.9 - - - +
35K LYS* 1.3 55.7 + - - +
36K ASN 3.7 1.6 - - - +
38K ARG 3.5 5.2 - - - +
39K LEU* 4.8 0.7 - - - +
61K ILE* 4.0 31.2 - - + +
64K MET* 3.8 17.5 - - + +
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Residues in contact with LYS 35 (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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12K PRO* 3.7 27.1 - - + +
13K THR* 3.2 29.5 + - - +
14K ALA 3.1 18.6 - - - +
15K VAL* 3.8 17.9 - - + -
16K ASN* 3.1 7.2 - - - -
33K ILE* 4.1 8.9 + - + -
34K ALA* 1.3 73.7 - - - +
36K ASN* 1.3 54.4 + - - +
37K THR 2.6 18.7 + - - -
38K ARG* 2.9 30.4 + - + +
40K GLU* 3.4 38.4 + - + +
331K SER* 6.2 0.2 - - - -
353K PHE* 5.7 6.7 - - - +
354K THR 5.2 3.2 + - - -
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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