Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 2JJ6
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 LYS 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 3.6 3.2 + - - +
15A LYS* 1.3 80.6 - - - +
17A VAL* 1.3 72.5 + - - +
18A LEU* 4.0 5.2 + - + +
90A GLU* 3.4 36.3 + - + +
91A ILE 3.3 14.1 - - - +
92A LEU* 4.3 20.6 - - + -
101A PHE* 5.6 5.8 - - - -
134A LEU* 6.0 0.3 - - - +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 15.0 - - + -
11A MET* 3.6 39.3 - - + -
15A LYS* 5.4 0.9 - - + -
16A LYS* 1.3 74.5 - - - +
18A LEU* 1.3 67.6 + - - +
19A VAL* 4.2 2.6 + - + +
34A LEU* 4.7 9.9 - - + -
89A VAL 3.8 0.7 - - - +
90A GLU* 3.2 5.4 - - - +
91A ILE* 2.8 45.6 + - + +
123A ILE* 4.3 26.5 - - + -
134A LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 4.0 5.7 + - + +
17A VAL* 1.3 77.0 - - - +
19A VAL* 1.3 64.5 + - - +
20A MET* 3.9 20.4 - - + -
88A ARG* 3.5 45.3 - - + +
89A VAL 3.5 1.6 - - - -
90A GLU* 3.6 19.7 - - + +
133A LYS* 5.3 3.4 - - + +
134A LEU* 2.6 64.8 - - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.6 5.4 - - + -
18A LEU* 1.3 79.4 - - - +
20A MET* 1.3 70.8 + - - +
32A ILE* 4.2 22.0 - - + -
87A PHE* 3.9 9.8 - - + -
88A ARG* 3.6 1.0 - - - -
89A VAL* 2.7 52.6 + - + +
91A ILE* 6.1 1.1 - - + -
123A ILE* 3.6 31.9 - - + -
125A ILE* 4.0 20.4 - - + -
129A LEU* 5.9 0.4 - - + -
131A ILE* 4.7 5.2 - - + -
133A LYS 3.8 2.5 - - - -
134A LEU* 4.0 10.3 - - - +
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.9 19.0 - - + -
19A VAL* 1.3 79.9 - - - +
21A GLY* 1.3 58.5 + - - +
87A PHE* 3.5 10.3 - - - +
88A ARG* 3.3 45.8 - - + +
131A ILE* 3.7 6.2 - - - +
132A THR* 2.8 29.5 + - - +
133A LYS* 3.1 52.1 + - + +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 5.7 0.2 - - - -
20A MET* 1.3 76.4 - - - +
22A ILE* 1.3 64.7 + - - +
86A PRO* 3.4 5.4 - - - +
87A PHE* 3.0 45.6 + - - +
130A GLN 2.9 14.4 - - - -
131A ILE* 4.1 1.3 - - - -
132A THR* 3.5 9.7 + - - -
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY* 1.3 79.7 - - - +
23A VAL* 1.3 70.2 + - - +
84A ASP* 3.7 24.5 - - - +
85A GLN 3.9 6.5 - - - -
86A PRO* 4.2 17.5 - - + -
87A PHE* 3.8 3.3 - - - -
129A LEU* 3.3 1.2 - - - -
130A GLN* 2.7 61.9 + - + +
132A THR* 4.0 20.6 - - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 1.3 79.1 - - - +
24A ASP* 1.3 72.2 + - - +
27A PRO* 3.7 12.1 - - + -
30A PHE* 4.3 5.6 - - + -
54A PHE* 3.5 25.4 - - + -
81A PHE* 4.2 19.3 - - + -
82A ILE 3.4 23.3 - - - +
83A PRO* 3.8 0.9 - - + -
84A ASP* 2.9 24.4 + - - +
85A GLN 3.3 15.6 + - - +
87A PHE* 3.7 20.2 - - + -
128A ASP 4.0 6.3 - - - +
129A LEU* 4.3 2.5 - - - -
130A GLN* 3.7 1.0 - - - +
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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