Contacts of the helix formed by residues 47 - 59 (chain D) in PDB entry 1CCW
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 ASN 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU 5.5 4.4 + - - -
42D ILE* 4.9 6.2 - - + +
43D PRO 3.4 6.7 + - - +
44D ALA* 3.0 8.2 + - - +
45D GLU 3.5 0.2 - - - -
46D LYS* 1.3 78.1 - - - +
48D PHE* 1.3 63.6 - - - +
49D ALA* 3.0 12.3 + - - +
50D GLU* 2.8 58.1 + - - +
51D LYS* 3.0 23.7 + - - +
145D PRO* 3.8 0.9 - - - -
168D THR* 3.6 16.7 - - + +
209D VAL* 5.5 2.8 - - - +
210D HIS* 2.9 24.9 + - - +
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Residues in contact with PHE 48 (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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47D ASN* 1.3 71.4 + - - +
49D ALA* 1.3 63.5 + - - +
51D LYS* 3.4 1.4 + - - +
52D LEU* 3.0 44.0 + - + +
64D GLN* 3.7 9.6 - - - -
90D PHE* 3.3 42.0 - + + -
91D LEU 4.1 2.9 - - - -
145D PRO* 3.5 22.9 - - + +
146D LEU 3.9 6.5 - - - -
147D GLN* 3.5 39.3 - - + -
168D THR* 2.8 31.7 + - - +
169D SER* 3.6 16.2 - - - -
212D ASN* 4.2 4.3 - - - -
322D LYS* 3.6 19.5 - - + -
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Residues in contact with ALA 49 (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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47D ASN* 3.0 9.1 + - - +
48D PHE* 1.3 79.3 - - - +
50D GLU* 1.3 62.4 + - - +
52D LEU* 3.3 3.7 + - - +
53D VAL* 3.2 18.7 + - - +
168D THR 4.2 2.0 + - - -
210D HIS* 3.9 31.0 - - + -
211D ILE 4.1 0.4 - - - +
212D ASN* 4.0 8.9 - - - +
247D ASN* 3.3 40.6 - - + +
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Residues in contact with GLU 50 (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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44D ALA* 3.2 38.1 - - + +
47D ASN* 2.8 31.3 + - - +
49D ALA* 1.3 73.2 - - - +
51D LYS* 1.3 65.5 + - - +
53D VAL* 3.2 18.3 + - + +
54D LEU* 3.2 12.6 + - - +
210D HIS* 3.4 30.8 + - + -
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Residues in contact with LYS 51 (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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44D ALA 4.5 5.3 + - - +
45D GLU* 4.3 9.0 + - - +
47D ASN 3.0 17.3 + - - +
49D ALA 3.3 0.2 - - - -
50D GLU* 1.3 74.2 - - - +
52D LEU* 1.3 66.5 + - - +
54D LEU* 3.3 16.7 + - + +
55D ALA* 3.0 21.5 + - - +
62D MET* 3.7 26.9 - - + -
89D ASP* 2.8 36.1 + - - +
90D PHE* 3.8 24.2 - - + -
144D LEU* 3.6 18.2 - - - +
145D PRO* 3.8 13.0 - - + +
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Residues in contact with LEU 52 (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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48D PHE* 3.0 27.8 + - + +
49D ALA 3.5 6.3 - - - +
51D LYS* 1.3 77.7 - - - +
53D VAL* 1.3 62.9 + - - +
55D ALA* 3.2 5.0 + - + +
56D LYS* 3.0 23.2 + - - +
90D PHE* 3.9 23.6 - - + -
212D ASN* 3.2 38.4 - - - +
247D ASN* 3.7 9.6 - - - +
249D THR* 3.4 12.6 - - + +
285D PHE* 4.6 1.6 - - + -
287D THR* 3.9 20.0 - - + +
321D THR* 4.1 20.3 - - + +
322D LYS* 4.7 9.2 - - + -
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Residues in contact with VAL 53 (chain D).
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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49D ALA 3.2 15.2 + - - +
50D GLU* 3.2 11.5 + - + +
52D LEU* 1.3 75.5 - - - +
54D LEU* 1.3 57.4 + - - +
56D LYS* 3.3 3.8 + - - +
57D LYS* 2.9 31.4 + - + +
247D ASN* 4.1 5.8 - - - +
285D PHE* 3.8 44.5 - - + -
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Residues in contact with LEU 54 (chain D).
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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50D GLU 3.2 9.3 + - - +
51D LYS* 3.4 24.2 - - + +
53D VAL* 1.3 77.7 - - - +
55D ALA* 1.3 59.4 + - - +
57D LYS* 3.1 12.0 + - + +
58D LYS* 2.8 71.3 + - + +
62D MET* 4.9 5.2 - - + -
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Residues in contact with ALA 55 (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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51D LYS 3.0 10.2 + - - +
52D LEU* 3.2 9.8 + - + +
54D LEU* 1.3 76.6 - - - +
56D LYS* 1.3 58.9 + - - +
58D LYS* 3.3 0.6 + - - -
59D GLY* 2.9 24.4 + - - -
60D ILE* 3.1 30.3 + - - +
62D MET* 3.7 33.6 - - + +
90D PHE* 5.8 0.2 - - + -
321D THR* 3.8 14.1 - - + +
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Residues in contact with LYS 56 (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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52D LEU 3.0 10.3 + - - +
53D VAL 3.4 8.3 - - - +
55D ALA* 1.3 78.9 - - - +
57D LYS* 1.3 62.1 + - - +
59D GLY* 3.3 11.9 + - - -
269D GLU* 2.6 36.3 + - - -
285D PHE* 3.8 29.2 - - + -
286D VAL 3.7 13.0 - - - -
287D THR* 3.9 6.1 - - + +
288D THR* 5.3 0.6 + - - -
319D GLY 4.8 8.7 + - - -
321D THR* 3.8 22.3 + - + +
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Residues in contact with LYS 57 (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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53D VAL* 2.9 17.7 + - + +
54D LEU* 3.4 18.6 - - + +
56D LYS* 1.3 77.3 - - - +
58D LYS* 1.3 67.1 + - + +
59D GLY 3.7 0.3 + - - -
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Residues in contact with LYS 58 (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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54D LEU* 2.8 57.4 + - + +
55D ALA 4.1 0.7 - - - +
57D LYS* 1.3 85.9 - - + +
59D GLY* 1.3 60.7 - - - +
60D ILE* 3.3 37.0 + - + +
62D MET* 5.3 2.2 - - - +
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Residues in contact with GLY 59 (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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55D ALA 2.9 7.4 + - - -
56D LYS* 3.3 10.8 + - - -
57D LYS 3.4 0.8 + - - -
58D LYS* 1.3 79.2 - - - +
60D ILE* 1.3 58.4 + - - +
61D THR 4.4 0.3 + - - -
356D GLY* 5.1 6.2 + - - -
358D ARG* 2.9 34.4 + - - -
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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