Contacts of the strand formed by residues 110 - 119 (chain J) in PDB entry 4CDC
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 TRP 110 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108G ARG* 6.1 0.4 - - - -
21J SER 3.7 0.2 - - - +
23J GLY 3.7 3.6 + - - -
24J SER* 2.8 32.4 + - - +
25J GLN 3.7 14.8 - - - +
26J ARG* 3.3 35.7 - - + +
28J VAL* 3.9 19.5 - - + -
101J TRP* 3.8 24.9 - + + -
102J VAL 3.3 7.0 - - - -
103J HIS* 3.4 35.4 - + + +
107J GLY* 3.0 31.1 + - - -
108J ARG 3.7 3.1 - - - -
109J ASN* 1.3 79.8 - - - +
111J ALA* 1.3 64.9 + - - +
270K TYR* 3.5 23.6 - - - -
289K ASP* 3.8 17.9 - - + -
290K PHE* 3.7 22.0 - + - -
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Residues in contact with ALA 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439I LEU* 5.0 3.4 - - + -
19J VAL* 3.7 13.0 - - + -
20J GLY 3.4 14.4 - - - +
21J SER* 3.7 10.8 - - - +
22J SER* 4.0 6.7 - - - -
23J GLY 4.9 0.2 - - - +
24J SER* 5.1 1.1 - - - -
28J VAL* 5.1 2.7 - - - -
30J CYS* 4.2 2.9 - - - -
101J TRP* 3.6 4.3 - - - +
102J VAL* 2.7 47.8 + - + +
110J TRP* 1.3 79.7 - - - +
112J CYS* 1.3 60.2 + - - +
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Residues in contact with CYS 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL* 3.5 3.8 - - - +
20J GLY 2.9 30.8 + - - +
21J SER* 4.4 10.1 - - - +
28J VAL* 3.8 14.6 - - - -
29J ASN 3.9 4.0 - - - -
30J CYS* 2.1 51.6 - - - -
33J MET* 4.0 16.6 - - + -
99J THR* 3.8 12.3 - - + -
100J GLY 3.2 7.0 - - - +
111J ALA* 1.3 75.9 - - - +
113J PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J PHE* 3.9 28.9 - + - -
18J GLN 3.1 17.3 - - - +
19J VAL* 4.1 2.5 - - + -
33J MET* 3.7 4.9 - - - -
68J PHE* 4.5 4.9 - + - -
77J TRP* 3.8 36.6 - + + -
78J PHE 3.3 34.1 - - - -
79J ALA* 3.6 17.9 - - + -
97J THR* 4.6 0.2 - - - -
98J MET 4.0 0.2 - - - +
99J THR* 3.4 2.8 - - - -
100J GLY 2.6 47.4 + - - -
101J TRP 3.4 23.3 - - - -
102J VAL* 3.9 4.0 - - + -
112J CYS* 1.3 78.1 - - - +
114J THR* 1.3 74.9 + - - +
115J GLY 4.6 1.6 - - - -
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Residues in contact with THR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J VAL 4.0 0.3 - - - +
17J PHE* 3.6 2.1 - - - -
18J GLN* 2.9 39.6 + - - +
33J MET* 3.2 27.3 - - + +
36J GLN* 4.9 2.9 + - - -
97J THR* 3.6 11.4 - - - +
98J MET 4.3 2.0 - - - +
99J THR* 3.7 25.8 - - - +
113J PHE* 1.3 81.7 - - - +
115J GLY* 1.3 59.5 + - - +
116J LYS* 5.8 2.1 - - - +
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Residues in contact with GLY 115 (chain J).
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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15J TRP* 4.0 5.6 - - - -
16J VAL 3.3 9.2 - - - -
17J PHE* 3.6 17.5 - - - -
96J GLU* 3.3 4.7 - - - +
97J THR* 2.8 38.0 + - - +
113J PHE* 4.3 0.2 - - - -
114J THR* 1.3 77.7 - - - +
116J LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J TRP* 3.6 4.5 - - - -
16J VAL* 2.9 40.1 + - + +
18J GLN* 6.2 4.3 - - + -
95J ASN 3.5 6.1 - - - +
96J GLU* 4.2 22.0 - - + +
114J THR* 5.8 2.7 - - - +
115J GLY* 1.3 78.6 - - - +
117J LYS* 1.3 64.7 + - - +
118J VAL 3.7 0.5 + - - -
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Residues in contact with LYS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J LEU 3.7 4.6 + - - -
10J ASP* 2.6 35.5 + - - +
12J LEU 2.7 27.7 + - - -
13J GLY* 4.5 0.2 - - - -
14J THR 3.3 16.4 - - - +
15J TRP* 3.6 23.0 - - + +
95J ASN* 2.8 38.7 + - + +
116J LYS* 1.3 76.7 - - - +
118J VAL* 1.3 63.6 + - - +
119J GLY* 3.7 25.8 - - - +
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Residues in contact with VAL 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J THR* 2.9 33.9 + - + +
16J VAL* 3.5 30.7 - - + -
116J LYS 3.7 0.2 + - - -
117J LYS* 1.3 73.7 - - - +
119J GLY* 1.3 59.7 - - - +
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Residues in contact with GLY 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LEU 5.0 0.4 - - - -
13J GLY* 3.6 8.4 - - - -
14J THR* 3.1 28.6 + - - -
117J LYS* 3.6 22.0 - - - +
118J VAL* 1.3 82.9 - - - +
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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