Contacts of the helix formed by residues 64 - 76 (chain D) in PDB entry 2H5X
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 ASP 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D ILE* 3.8 10.0 - - - +
62D PHE* 3.4 1.2 - - - +
63D PRO* 1.3 87.4 - - - +
65D GLY* 1.3 65.0 + - - +
66D GLU* 3.2 26.4 - - - +
67D THR* 2.5 48.7 + - - -
68D ARG* 3.1 18.4 + - - +
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Residues in contact with GLY 65 (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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11C GLU* 6.1 0.9 - - - -
47D ILE* 3.8 22.0 - - - +
64D ASP* 1.3 72.9 - - - +
66D GLU* 1.3 71.7 + - - +
68D ARG* 3.0 11.4 + - - +
69D ASP* 2.9 31.4 + - - -
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Residues in contact with GLU 66 (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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64D ASP* 3.2 26.5 - - - +
65D GLY* 1.3 85.1 + - - +
67D THR* 1.3 65.0 + - - +
69D ASP* 3.1 15.2 + - - +
70D LEU 3.2 9.4 + - - -
98D ARG* 3.9 18.3 + - - +
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Residues in contact with THR 67 (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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62D PHE* 3.7 28.9 - - + -
63D PRO* 4.8 5.9 - - + +
64D ASP* 2.5 38.2 + - - -
66D GLU* 1.3 73.4 - - - +
68D ARG* 1.3 61.7 + - - +
70D LEU* 3.2 8.6 + - + +
71D PHE* 3.1 20.4 + - - +
89D LEU* 4.6 10.3 - - + +
93D ASP* 5.9 0.9 - - - +
94D ALA* 4.0 27.6 - - + +
98D ARG* 5.3 0.7 - - - +
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Residues in contact with ARG 68 (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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11C GLU* 5.1 8.3 + - - -
16C HIS* 6.2 1.2 - - - -
18C VAL* 6.1 1.8 - - - +
27C ARG* 5.6 6.0 - - - +
3D ALA* 3.4 18.8 + - - +
47D ILE* 3.3 31.1 - - + +
48D THR 2.5 47.9 + - - +
49D ALA* 4.0 11.9 - - + +
62D PHE* 3.5 25.5 - - + -
64D ASP 3.1 11.4 + - - +
65D GLY* 3.0 13.8 + - - +
67D THR* 1.3 77.3 - - - +
69D ASP* 1.3 82.3 + - - +
71D PHE* 3.3 15.1 - - - +
72D LEU* 3.4 19.4 + - - +
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Residues in contact with ASP 69 (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 GLY 2.9 16.2 + - - +
66D GLU* 3.5 9.9 - - - +
67D THR 3.1 0.2 - - - -
68D ARG* 1.3 102.3 + - - +
70D LEU* 1.3 64.6 + - - +
71D PHE 3.1 1.6 - - - -
72D LEU* 3.2 13.0 + - - +
73D THR* 3.0 26.0 + - - +
98D ARG* 5.9 0.4 - - - +
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Residues in contact with LEU 70 (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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66D GLU 3.2 7.1 + - - +
67D THR* 3.6 9.2 - - - +
69D ASP* 1.3 76.7 - - - +
71D PHE* 1.3 62.9 + - - +
73D THR* 3.3 14.7 + - + -
74D LEU* 3.1 34.0 + - + +
89D LEU* 4.0 16.4 - - + -
94D ALA* 3.9 38.6 - - + +
97D LEU* 4.3 9.0 - - + -
98D ARG* 3.8 41.0 - - + +
101D LEU* 5.4 3.6 - - + -
127D LEU* 6.2 0.4 - - + -
130D LYS 5.9 0.2 - - - +
131D VAL* 4.3 15.5 - - + -
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Residues in contact with PHE 71 (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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49D ALA* 3.6 25.8 - - + -
51D ILE* 4.5 2.2 - - + -
60D TYR* 3.6 38.8 - + + -
62D PHE* 3.4 27.4 - + + -
67D THR 3.1 9.4 + - - +
68D ARG 3.3 9.4 - - - +
69D ASP 3.1 0.4 - - - -
70D LEU* 1.3 77.5 - - - +
72D LEU* 1.3 62.0 + - + +
74D LEU* 3.2 24.1 + - - +
75D LEU* 3.4 25.0 + - + +
82D PRO* 4.2 14.6 - - + -
85D ALA* 3.4 27.1 - - + -
86D MET* 3.8 21.1 - - + -
89D LEU* 4.3 9.2 - - + -
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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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49D ALA* 3.8 23.6 - - + -
50D MET 5.8 0.2 - - - +
51D ILE* 4.2 9.0 - - + -
68D ARG* 3.6 29.4 - - - +
69D ASP* 3.2 14.0 + - - +
71D PHE* 1.3 79.4 - - - +
73D THR* 1.3 62.8 + - - +
75D LEU* 3.0 38.1 + - + +
76D SER* 3.2 7.3 + - - -
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Residues in contact with THR 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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69D ASP* 3.0 14.9 + - - +
70D LEU* 3.4 20.2 - - + +
72D LEU* 1.3 77.2 - - - +
74D LEU* 1.3 60.6 + - - +
76D SER* 2.5 29.4 + - - +
77D VAL* 4.0 0.2 - - - +
127D LEU* 3.5 29.7 - - + +
130D LYS* 4.2 22.1 + - + +
131D VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 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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70D LEU* 3.1 22.9 + - + +
71D PHE* 3.4 9.9 - - - +
72D LEU 3.2 0.2 - - - -
73D THR* 1.3 75.6 - - - +
75D LEU* 1.3 64.9 + - - +
77D VAL* 3.0 20.5 + - + +
80D VAL* 3.4 17.8 - - + +
85D ALA* 3.7 37.7 - - + +
88D ALA* 4.7 5.6 - - + -
89D LEU* 4.3 8.5 - - + -
97D LEU* 4.1 24.2 - - + -
101D LEU* 4.4 13.9 - - + -
123D MET* 5.2 11.7 - - - -
127D LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 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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51D ILE* 3.8 30.1 - - + -
53D ARG* 6.3 0.2 - - - +
71D PHE* 3.5 25.6 - - + +
72D LEU* 3.0 22.9 + - + +
74D LEU* 1.3 71.7 - - - +
76D SER* 1.3 56.4 + - - +
77D VAL 2.9 17.9 + - - +
80D VAL 3.5 9.2 - - - +
81D GLY* 3.4 35.7 - - - +
82D PRO* 3.4 14.4 - - + -
85D ALA* 3.9 8.7 - - + -
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Residues in contact with SER 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 3.2 7.5 + - - -
73D THR* 2.5 26.8 + - - +
75D LEU* 1.3 77.6 - - - +
77D VAL* 1.3 61.5 + - - +
78D SER 3.8 1.0 + - - -
126D GLU* 3.3 15.3 + - - +
127D LEU* 4.2 5.5 - - - +
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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