Contacts of the helix formed by residues 71 - 85 (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 LEU 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.5 2.4 - - - +
70D ALA* 1.3 85.2 - - + +
72D LEU* 1.3 60.6 + - - +
73D ASP 3.5 0.2 - - - -
74D GLU* 3.2 34.3 + - + +
75D HIS* 2.8 32.7 + - - +
111D ILE* 3.7 40.2 - - + +
114D SER* 4.2 11.7 - - - +
115D GLU* 3.7 35.4 - - + +
118D GLY 6.5 0.2 - - - -
119D ARG 6.3 0.4 - - - -
120D SER* 5.7 0.4 - - - -
130D PHE* 3.8 2.9 - - + -
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Residues in contact with LEU 72 (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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71D LEU* 1.3 73.1 - - - +
73D ASP* 1.3 70.2 + - - +
75D HIS* 3.2 2.9 + - - +
76D ILE* 3.0 35.5 + - + +
125D PHE* 3.8 16.8 - - + -
130D PHE* 3.5 24.7 - - + -
133D LYS* 6.4 0.4 - - + -
134D GLY* 3.6 37.7 - - - +
137D LYS* 4.2 20.6 - - + -
138D VAL* 3.7 20.0 - - + -
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Residues in contact with ASP 73 (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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71D LEU 3.5 0.4 - - - -
72D LEU* 1.3 84.2 - - - +
74D GLU* 1.3 67.4 + - - +
76D ILE* 3.4 14.2 + - - +
77D GLU* 3.0 28.7 + - - +
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Residues in contact with GLU 74 (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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69D VAL* 3.7 12.9 - - + +
71D LEU* 3.2 40.1 - - + +
72D LEU 3.3 0.4 - - - -
73D ASP* 1.3 82.3 + - - +
75D HIS* 1.3 60.8 + - - +
77D GLU* 3.3 13.6 + - - +
78D LEU* 2.9 29.5 + - - +
118D GLY 6.2 0.3 - - - -
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Residues in contact with HIS 75 (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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67D ALA 3.9 4.0 - - - -
68D GLY* 3.5 19.7 - - - -
69D VAL* 3.4 28.1 + - + +
71D LEU 2.8 18.9 + - - +
72D LEU 3.2 3.8 + - - +
74D GLU* 1.3 78.9 - - - +
76D ILE* 1.3 61.3 + - - +
78D LEU* 3.3 5.2 + - - +
79D LEU* 2.9 42.4 + - + +
93D SER* 3.3 31.8 + - - -
125D PHE* 3.4 39.1 - + + -
138D VAL* 3.9 21.1 - - + +
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Residues in contact with ILE 76 (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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72D LEU* 3.0 28.2 + - + +
73D ASP* 3.6 15.0 - - - +
75D HIS* 1.3 75.8 - - - +
77D GLU* 1.3 57.1 + - - +
79D LEU* 3.3 5.4 + - - +
80D ARG* 2.9 50.7 + - + +
137D LYS* 3.8 29.6 - - + +
138D VAL* 4.0 24.5 - - + +
141D ALA* 3.5 23.8 - - + -
142D VAL* 5.1 1.7 - - + +
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Residues in contact with GLU 77 (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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73D ASP 3.0 16.6 + - - +
74D GLU* 3.3 13.1 + - - +
76D ILE* 1.3 76.1 - - - +
78D LEU* 1.3 62.7 + - - +
80D ARG* 3.4 10.5 + - - +
81D TYR* 3.0 24.1 + - + +
337D LYS* 4.5 21.0 + - + -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ALA* 4.0 13.7 - - + -
68D GLY* 3.9 27.1 - - - +
69D VAL* 4.0 23.8 - - + -
74D GLU 2.9 17.0 + - - +
75D HIS* 3.4 7.0 - - - +
77D GLU* 1.3 78.1 - - - +
79D LEU* 1.3 63.9 + - + +
81D TYR* 3.2 7.3 + - - +
82D LEU* 3.0 37.4 + - + +
335D PRO 5.5 3.4 - - - +
336D THR 5.1 0.9 - - - -
337D LYS* 3.7 36.1 - - + +
340D ASN* 5.3 2.5 - - - +
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Residues in contact with LEU 79 (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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67D ALA* 4.2 23.1 - - + -
75D HIS* 2.9 36.1 + - + +
76D ILE 3.9 3.6 - - - +
78D LEU* 1.3 77.4 - - + +
80D ARG* 1.3 63.4 + - - +
82D LEU* 3.2 9.8 + - + +
83D GLN* 2.9 25.1 + - - +
91D LEU* 3.8 11.8 - - + +
92D PRO* 3.6 31.9 - - + +
93D SER* 3.8 1.8 - - - +
138D VAL* 3.6 31.4 - - + -
142D VAL* 4.1 14.1 - - + -
146D LEU* 3.9 9.2 - - + -
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Residues in contact with ARG 80 (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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76D ILE* 2.9 40.6 + - + +
77D GLU* 3.7 8.4 - - - +
78D LEU 3.3 0.2 - - - -
79D LEU* 1.3 75.6 - - - +
81D TYR* 1.3 57.5 + - - +
83D GLN* 3.3 11.6 + - - +
84D ASP* 2.8 46.7 + - - +
141D ALA* 3.1 41.2 + - - +
142D VAL* 4.6 4.9 - - + -
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Residues in contact with TYR 81 (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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77D GLU* 3.0 15.4 + - + +
78D LEU 3.4 9.4 - - - +
80D ARG* 1.3 77.8 - - - +
82D LEU* 1.3 59.3 + - + +
84D ASP* 4.7 1.3 - - - -
85D GLU* 2.8 62.6 + - + +
86D GLY 3.1 5.0 + - - -
337D LYS* 3.6 68.9 - - + -
338D GLU* 3.8 17.1 - - + +
341D ALA* 3.7 17.0 - - + +
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Residues in contact with LEU 82 (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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65D PRO* 3.9 14.8 - - + -
67D ALA* 3.5 32.3 - - + -
78D LEU* 3.0 26.4 + - + +
79D LEU* 3.2 13.0 + - + +
81D TYR* 1.3 77.5 - - + +
83D GLN* 1.3 56.9 + - - +
86D GLY* 3.2 7.9 - - - +
87D GLY 3.1 22.3 + - - -
88D ALA* 3.1 11.3 + - + +
91D LEU* 4.3 8.3 - - + -
337D LYS* 3.8 13.5 - - - +
340D ASN* 3.6 35.7 - - + +
341D ALA* 4.0 6.5 - - - +
344D ILE* 4.0 9.8 - - + +
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Residues in contact with GLN 83 (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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79D LEU 2.9 16.0 + - - +
80D ARG* 3.5 10.1 + - - +
82D LEU* 1.3 77.8 - - - +
84D ASP* 1.3 82.4 + - - +
87D GLY* 3.2 21.8 + - - -
88D ALA* 3.8 4.4 + - - +
91D LEU* 4.0 3.4 - - + +
141D ALA 5.2 0.8 + - - -
142D VAL* 3.7 13.4 - - - +
143D ASN* 2.8 55.4 + - + +
144D LEU* 3.6 32.2 - - + +
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Residues in contact with ASP 84 (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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80D ARG* 2.8 31.5 + - - +
81D TYR* 4.7 1.3 - - - -
83D GLN* 1.3 104.5 + - - +
85D GLU* 1.3 66.2 + - + +
87D GLY* 4.1 3.6 + - - -
143D ASN* 5.2 0.3 + - - -
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Residues in contact with GLU 85 (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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81D TYR* 2.8 59.9 + - + +
84D ASP* 1.3 80.2 - - + +
86D GLY* 1.3 60.9 + - - +
87D GLY 3.7 0.2 + - - -
341D ALA* 4.4 2.9 - - + -
345D LYS* 3.7 27.0 + - - +
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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