Contacts of the helix formed by residues 44 - 56 (chain C) 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 HIS 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C LYS 5.6 0.6 + - - -
42C LEU 3.9 0.8 - - - -
43C CYS* 1.3 100.0 + - + +
45C PRO* 1.3 68.4 - - - +
46C GLU* 3.0 14.6 - - + +
47C GLU* 2.9 50.4 + - + +
48C LEU* 4.0 4.5 + - - +
152C VAL* 5.2 1.1 - - - -
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Residues in contact with PRO 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 5.0 7.9 - - - +
43C CYS 3.6 9.2 - - - +
44C HIS* 1.3 82.7 - - - +
46C GLU* 1.3 84.4 + - - +
48C LEU* 2.9 19.3 + - + +
49C VAL* 3.1 13.2 + - - +
152C VAL* 3.8 29.3 - - + -
153C LEU* 4.3 8.1 - - + +
156C SER* 3.9 26.2 - - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS* 2.9 15.3 + - + +
45C PRO* 1.3 103.9 - - - +
47C GLU* 1.3 63.8 + - + +
49C VAL* 3.1 33.0 + - + +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C CYS 5.6 0.9 + - - -
44C HIS* 2.9 44.3 + - + +
46C GLU* 1.3 79.2 - - + +
48C LEU* 1.3 67.4 + - + +
49C VAL 3.8 0.2 + - - -
50C LEU* 5.0 2.6 + - - +
51C LEU* 5.8 1.4 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.9 31.6 - - + -
44C HIS 4.6 6.1 - - - +
45C PRO* 2.9 9.9 + - + +
47C GLU* 1.3 87.4 - - + +
49C VAL* 1.3 67.0 + - - +
50C LEU* 3.1 3.1 - - - -
51C LEU* 2.8 44.3 + - + +
52C GLY 4.1 1.0 + - - -
145C PHE* 4.6 8.3 - - + -
149C ALA* 3.9 22.0 - - + +
152C VAL* 4.3 21.5 - - + -
153C LEU* 4.2 17.3 - - + +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PRO 3.1 8.7 + - - +
46C GLU* 3.1 36.7 + - + +
47C GLU 3.4 0.6 - - - -
48C LEU* 1.3 73.9 - - - +
50C LEU* 1.3 74.5 + - + +
51C LEU 3.1 1.9 + - - -
52C GLY* 3.1 14.9 + - - -
53C HIS 4.7 0.3 + - - -
153C LEU* 4.8 6.9 - - + +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU 5.0 2.4 + - - +
48C LEU 2.9 3.6 + - - -
49C VAL* 1.3 84.4 - - + +
51C LEU* 1.3 71.2 + - + +
52C GLY 3.2 0.2 - - - -
53C HIS* 3.3 22.9 - - - +
54C SER* 4.0 3.3 + - - -
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU 5.8 0.9 - - - +
48C LEU* 2.8 45.2 + - + +
50C LEU* 1.3 80.3 - - + +
52C GLY* 1.3 59.6 + - - +
53C HIS 2.8 6.8 + - - -
54C SER* 3.1 15.9 + - - +
55C LEU* 2.9 38.2 + - + +
145C PHE* 4.0 23.8 - - + -
149C ALA* 4.4 8.1 - - + -
153C LEU* 4.3 10.3 - - + -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU 4.1 1.2 + - - -
49C VAL 3.1 13.3 + - - -
51C LEU* 1.3 76.3 - - - +
53C HIS* 1.3 55.4 + - - +
56C GLY* 3.3 4.5 + - - -
57C ILE* 2.9 43.9 + - - +
153C LEU* 4.1 14.1 - - - +
157C HIS* 5.7 5.2 - - - -
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Residues in contact with HIS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL 4.7 0.2 + - - -
50C LEU* 3.3 14.0 + - + +
51C LEU 2.8 0.4 - - - -
52C GLY* 1.3 75.7 - - - +
54C SER* 1.3 66.2 + - - +
56C GLY* 2.9 15.2 + - - -
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU 4.5 5.2 + - - -
51C LEU* 3.1 21.1 + - - +
53C HIS* 1.3 79.5 - - - +
55C LEU* 1.3 69.2 + - - +
56C GLY 3.7 0.2 + - - -
146C GLN* 5.4 1.5 + - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 2.9 31.0 + - + +
54C SER* 1.3 84.3 - - - +
56C GLY* 1.3 63.4 + - - +
57C ILE* 4.2 15.4 - - + +
139C PRO* 3.0 21.5 - - - +
140C ALA 4.6 11.1 + - - +
141C PHE* 4.4 9.9 - - + -
145C PHE* 6.5 0.2 - - + -
146C GLN* 3.0 68.6 - - + +
149C ALA* 4.7 4.9 - - + -
150C GLY* 4.3 11.7 - - - +
153C LEU* 4.9 2.0 - - + -
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Residues in contact with GLY 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLY 3.3 5.5 + - - -
53C HIS 2.9 14.1 + - - -
54C SER 3.4 0.4 + - - -
55C LEU* 1.3 77.6 - - - +
57C ILE* 1.3 61.3 + - - +
58C PRO* 3.4 6.7 - - - +
139C PRO* 3.0 25.6 - - - +
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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