Contacts of the strand formed by residues 9 - 16 (chain D) in PDB entry 1CD9
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 SER 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D SER 4.8 2.6 + - - -
8D PRO* 1.3 75.2 - - - +
10D ASN* 1.3 73.0 + - - +
11D LEU* 3.1 6.4 + - - -
26D TRP* 3.8 2.3 - - - +
27D GLU* 2.9 42.7 + - - +
96D SER* 5.5 0.2 - - - -
97D PRO* 5.7 2.5 - - - -
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Residues in contact with ASN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 1.3 80.3 - - - +
11D LEU* 1.3 62.2 + - - +
12D SER* 3.6 8.4 + - - -
25D GLN* 3.7 6.8 - - - +
26D TRP* 4.0 4.2 - - - -
27D GLU* 4.7 7.6 - - + -
923D NAG 1.5 76.8 + - - +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO 6.3 0.2 - - - -
9D SER* 3.1 5.8 + - - +
10D ASN* 1.3 77.8 - - - +
12D SER* 1.3 60.1 + - - +
13D CYS* 4.7 1.3 - - - -
24D CYS* 4.3 20.2 - - + -
25D GLN 3.4 14.8 - - - +
26D TRP* 4.3 11.9 - - + +
40D LEU* 4.6 6.1 - - + -
83D ILE* 3.9 24.7 - - + +
84D TRP* 4.2 4.7 - - - -
85D VAL* 4.3 16.8 - - + -
96D SER* 4.0 23.1 - - - +
97D PRO 4.4 4.9 - - - +
99D LEU* 3.7 32.8 - - + +
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Residues in contact with SER 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASN* 3.6 7.2 + - - -
11D LEU* 1.3 74.6 - - - +
13D CYS* 1.3 69.1 + - - +
14D LEU* 5.5 4.5 - - - +
23D VAL 3.8 0.4 - - - +
24D CYS* 3.1 3.5 - - - +
25D GLN* 3.0 53.0 + - - +
99D LEU* 4.6 3.6 - - - -
923D NAG 5.3 7.1 - - - -
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Residues in contact with CYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.7 2.9 - - - -
12D SER* 1.3 79.0 - - - +
14D LEU* 1.3 69.0 + - - +
22D LEU* 4.0 8.7 - - + -
23D VAL 3.1 5.2 - - - -
24D CYS* 2.0 46.9 - - - -
83D ILE* 4.0 21.5 - - - -
99D LEU* 4.6 8.7 - - - +
101D LEU* 3.7 20.7 - - + +
106D VAL* 3.5 20.8 - - - +
199D PHE* 5.0 1.6 - - - -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 5.5 5.2 - - - +
13D CYS* 1.3 81.5 - - - +
15D MET* 1.3 62.0 + - - +
16D HIS* 3.4 20.6 + - + -
22D LEU* 4.0 3.6 - - - -
23D VAL* 2.9 31.1 + - + +
25D GLN* 6.1 2.9 - - - +
106D VAL 3.2 14.8 - - - +
108D LYS* 4.1 34.5 - - + +
199D PHE* 3.7 28.0 - - + -
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Residues in contact with MET 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 6.2 0.2 - - - +
14D LEU* 1.3 69.6 - - - +
16D HIS* 1.3 63.0 + - - +
17D LEU* 3.6 9.1 + - + -
20D ASN* 3.6 30.5 - - - +
21D SER* 3.9 28.0 - - - +
22D LEU* 4.1 8.8 - - + +
72D ARG* 4.5 2.5 - - + -
75D LEU* 4.3 6.7 - - + -
77D LEU* 4.4 17.5 - - + -
103D PRO* 3.1 45.8 - - - +
104D MET* 4.4 6.1 - - - -
106D VAL 2.7 12.3 + - - +
107D VAL* 3.5 17.9 - - + +
108D LYS* 3.0 21.5 + - - +
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Residues in contact with HIS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.4 23.8 + - + -
15D MET* 1.3 71.6 - - - +
17D LEU* 1.3 56.4 + - - +
18D THR* 3.2 13.2 - - - +
19D THR* 3.4 21.1 - - + +
20D ASN* 2.7 36.4 + - - -
21D SER 2.9 14.1 + - - +
23D VAL* 3.8 28.0 - - + +
108D LYS* 3.4 40.4 + - + +
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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