Contacts of the strand formed by residues 26 - 34 (chain U) in PDB entry 4PJO
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 26 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U SER* 5.4 4.5 - - - +
19U LEU 3.1 15.3 - - - +
20U LYS* 4.5 6.7 - - + -
21U LEU* 4.9 0.2 - - - -
24U GLY 3.8 11.6 + - - -
25U ARG* 1.3 78.7 - - - +
27U VAL* 1.3 59.1 + - - +
47U GLU 2.3 30.0 - - - +
48U MET* 3.5 40.5 + - + +
49U ALA* 5.4 1.3 - - - -
50U THR* 5.3 7.9 + - - +
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Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S TRP* 3.6 36.6 - - + -
86S LEU* 4.4 3.8 - - + -
18U SER* 3.6 0.7 + - - -
19U LEU* 2.6 44.7 + - + +
21U LEU* 4.0 18.3 - - + +
26U HIS* 1.3 81.0 - - - +
28U GLN* 1.3 62.2 + - - +
42U ILE* 5.4 1.6 - - + -
45U CYS* 2.8 39.0 - - - -
46U VAL 3.6 7.4 - - - +
47U GLU* 3.7 6.5 - - + +
48U MET* 4.6 0.9 - - - -
62U ILE* 5.1 9.9 - - + -
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Residues in contact with GLN 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U LYS* 3.5 30.4 - - - +
17U LEU 3.1 13.0 - - - +
18U SER* 4.0 10.0 - - - +
19U LEU* 5.4 1.8 - - - -
27U VAL* 1.3 83.2 - - - +
29U GLY* 1.3 58.9 + - - +
42U ILE* 4.6 1.1 - - - -
45U CYS* 3.2 3.3 - - - +
46U VAL* 2.7 41.9 + - + +
48U MET* 2.8 44.1 - - + +
73U LEU* 3.7 16.9 - - + +
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Residues in contact with GLY 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LYS 3.5 0.5 - - - +
16U LYS* 4.0 8.5 - - - +
17U LEU* 2.6 46.2 + - - +
19U LEU* 5.9 0.8 - - - +
28U GLN* 1.3 77.1 - - - +
30U ILE* 1.3 64.3 + - - -
31U LEU 3.8 0.2 + - - -
42U ILE* 3.5 16.3 - - - +
43U ASP 3.7 6.3 - - - -
44U GLU 3.8 6.5 - - - -
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Residues in contact with ILE 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U ASP* 3.7 33.9 - - + +
15U LYS 3.2 2.5 - - - -
16U LYS* 4.0 26.5 - - + +
29U GLY* 1.3 74.8 - - - -
31U LEU* 1.3 64.0 + - - +
32U ARG* 3.2 9.4 + - + +
42U ILE* 3.5 2.3 - - - +
43U ASP* 2.8 49.4 + - + +
44U GLU* 3.6 37.9 - - + +
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Residues in contact with LEU 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U LEU* 4.1 23.8 - - + +
12U PHE* 3.6 32.8 - - + +
13U MET* 3.6 5.4 - - - +
14U ASP* 2.8 29.8 + - - -
15U LYS 3.0 8.3 + - - -
17U LEU* 3.5 27.1 - - + -
29U GLY 3.8 1.4 + - - -
30U ILE* 1.3 69.7 - - - +
32U ARG* 1.3 58.3 + - - +
33U GLY 3.3 29.6 - - - +
34U PHE* 4.6 4.3 - - + -
40U LEU* 4.1 15.7 - - + -
41U VAL 3.4 11.4 - - - +
42U ILE* 3.8 13.7 - - + -
70U LEU* 5.4 0.2 - - + -
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Residues in contact with ARG 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S MET* 3.7 19.3 - - - +
15S VAL* 3.3 61.2 + - + +
13U MET* 3.6 10.5 - - - +
14U ASP* 3.1 30.6 + - - -
30U ILE* 3.2 8.9 + - + +
31U LEU* 1.3 74.7 - - - +
33U GLY* 1.3 58.0 + - - +
41U VAL* 2.9 25.0 + - + -
43U ASP* 4.3 24.0 + - + +
59U MET* 5.0 1.8 - - - -
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Residues in contact with GLY 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S MET* 3.8 7.9 - - - -
15S VAL 3.1 16.5 + - - -
13U MET* 3.9 6.5 - - - -
31U LEU* 3.3 11.8 - - - +
32U ARG* 1.3 81.4 - - - +
34U PHE* 1.3 66.7 + - - +
40U LEU* 3.4 0.9 - - - -
41U VAL* 2.8 32.2 + - - +
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Residues in contact with PHE 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S MET* 3.1 33.8 - - + +
16S GLN* 4.4 0.5 - - - +
17S PRO* 3.9 9.9 - - - +
6U PRO* 5.0 7.2 - - + -
7U PRO* 3.6 27.4 - - + -
9U LEU* 3.3 44.4 - - + -
10U LYS* 3.9 28.0 - - + -
13U MET* 3.6 24.2 - - + -
31U LEU* 4.6 3.6 - - + -
33U GLY* 1.3 75.9 - - - +
35U ASP* 1.3 76.2 + - - +
39U ASN 3.1 13.9 - - - +
40U LEU* 3.6 14.1 - - + -
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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