Contacts of the strand formed by residues 19 - 25 (chain U) in PDB entry 2AK4
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 MET 19 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8U PRO* 5.2 2.9 - - + -
11U GLN* 3.5 31.6 - - + +
13U LEU* 3.4 14.8 - - + +
18U SER* 1.3 79.8 - - - +
20U THR* 1.3 66.7 + - - +
21U LEU* 3.6 36.6 - - + +
78U ARG* 3.5 5.6 - - - +
79U LEU* 3.1 43.5 + - + +
114U LEU* 3.4 34.1 - - + -
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Residues in contact with THR 20 (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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7U THR 4.6 1.6 - - - +
8U PRO* 4.9 4.2 - - - +
19U MET* 1.3 82.4 - - - +
21U LEU* 1.3 63.7 + - - +
22U GLN* 3.9 25.4 + - - +
76U SER* 3.9 20.6 - - - -
77U LEU 3.4 8.6 + - - -
78U ARG* 3.7 31.4 + - - +
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Residues in contact with LEU 21 (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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7U THR 3.8 1.8 - - - +
8U PRO* 3.7 22.2 - - + -
11U GLN* 5.6 0.4 - - + -
19U MET* 3.6 29.6 - - + -
20U THR* 1.3 72.7 + - - +
22U GLN* 1.3 61.9 + - - +
34U TRP* 3.8 18.6 - - + -
76U SER* 3.5 6.2 - - - -
77U LEU* 2.7 52.6 + - + +
79U LEU* 4.9 1.1 - - + -
90U TYR* 3.7 40.8 - - + -
112U THR* 3.4 24.0 - - + +
114U LEU* 5.0 2.0 - - + -
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Residues in contact with GLN 22 (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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5U THR 5.4 0.2 - - - -
6U GLN* 3.3 9.2 - - - +
7U THR* 3.0 50.7 + - - +
20U THR* 4.1 26.7 + - - +
21U LEU* 1.3 75.9 - - - +
23U CYS* 1.3 61.2 + - - +
34U TRP* 4.2 2.5 - - - -
74U GLU* 4.9 9.5 - - - +
75U PHE 4.6 0.2 - - - -
76U SER* 3.0 24.7 + - - -
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Residues in contact with CYS 23 (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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4U VAL* 3.8 14.6 - - - -
5U THR 3.4 4.3 - - - +
22U GLN* 1.3 76.0 + - - +
24U ALA* 1.3 62.1 + - - +
32U MET* 3.7 15.3 - - - -
34U TRP* 3.5 9.2 - - + -
73U ARG 3.8 0.3 - - - +
74U GLU* 3.3 7.0 - - - +
75U PHE 2.9 45.1 + - - +
92U CYS* 2.0 51.4 - - + -
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Residues in contact with ALA 24 (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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3U GLY 4.0 0.7 - - - +
4U VAL* 3.2 6.8 - - - +
5U THR* 2.8 46.9 + - - +
23U CYS* 1.3 74.8 - - - +
25U GLN* 1.3 61.7 + - - +
32U MET* 4.3 1.8 - - - -
73U ARG* 3.3 34.5 - - - +
74U GLU* 4.5 7.0 - - + -
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Residues in contact with GLN 25 (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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3U GLY 4.1 4.9 - - - -
4U VAL* 4.6 5.6 - - + -
24U ALA* 1.3 76.8 - - - +
26U ASP* 1.3 59.5 + - - +
27U MET* 2.8 31.0 + - + +
28U ASN* 2.5 35.5 + - - -
29U HIS* 2.9 35.1 + - - +
32U MET* 3.7 23.5 - - + +
72U LYS 3.4 17.4 + - - -
73U ARG* 2.9 30.4 + - - +
94U SER* 3.8 8.1 - - - +
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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