Contacts of the helix formed by residues 64 - 83 (chain D) in PDB entry 4HHM
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 64 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLY 3.6 1.9 + - - -
63D ALA* 1.3 75.2 - - - +
65D ASP* 1.3 56.4 + - - +
66D THR* 3.5 9.3 + - - -
67D GLU* 2.7 40.8 + - - +
68D ARG* 2.7 35.7 + - - +
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA 5.2 0.9 - - - +
64D SER* 1.3 74.1 - - - +
66D THR* 1.3 61.7 + - - +
68D ARG* 3.8 8.2 - - - +
69D GLU* 3.3 22.7 + - - +
121D ARG* 3.2 29.5 + - - +
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D SER* 3.0 8.9 + - - -
65D ASP* 1.3 77.6 - - - +
67D GLU* 1.3 66.0 + - + +
69D GLU* 3.4 7.2 + - - +
70D ALA* 3.2 20.4 + - + +
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLY 4.4 2.1 - - - +
63D ALA* 3.5 13.7 - - + -
64D SER* 2.7 43.2 + - - +
66D THR* 1.3 75.5 - - + +
68D ARG* 1.3 65.0 + - - +
70D ALA* 3.2 7.5 + - - +
71D HIS* 2.8 40.8 + - + +
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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
----------------------------------------------------------
357C TYR* 5.3 1.0 + - - -
55D ASP* 5.2 7.3 - - - +
59D ILE* 3.8 44.1 - - + +
63D ALA* 4.5 1.9 - - + +
64D SER 2.7 19.7 + - - +
65D ASP* 3.8 7.2 - - - +
67D GLU* 1.3 73.6 - - - +
69D GLU* 1.3 63.5 + - - +
70D ALA 3.2 0.2 + - - -
71D HIS* 3.3 3.3 + - - +
72D VAL* 3.2 31.0 + - + +
121D ARG* 3.4 64.1 + - - +
122D ASN* 4.8 10.3 + - - +
125D LEU* 4.0 31.7 - - - +
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Residues in contact with GLU 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 ASP 3.3 14.7 + - - +
66D THR* 3.6 7.0 - - - +
67D GLU 3.3 0.2 - - - -
68D ARG* 1.3 81.1 - - - +
70D ALA* 1.3 60.2 + - - +
72D VAL* 2.9 34.4 - - - +
73D LYS* 3.2 16.4 + - + +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D THR* 3.2 13.5 + - + +
67D GLU* 3.5 12.1 - - - +
68D ARG 3.2 0.6 - - - -
69D GLU* 1.3 76.9 - - - +
71D HIS* 1.3 67.9 + - + +
73D LYS* 3.2 8.0 + - - +
74D ARG* 3.1 31.7 + - + +
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LEU* 3.6 26.8 + - + +
59D ILE* 4.3 7.4 - - + -
60D PRO* 3.4 33.8 - - + +
63D ALA* 4.9 1.3 - - + +
67D GLU* 2.8 41.8 + - + +
68D ARG* 3.3 6.3 + - - +
70D ALA* 1.3 79.8 - - + +
72D VAL* 1.3 59.9 + - - +
74D ARG* 3.4 19.8 + - - +
75D PHE* 3.2 22.9 + - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LEU* 4.4 5.4 - - + -
59D ILE* 3.8 24.5 - - + -
68D ARG* 3.2 17.9 + - + +
69D GLU* 2.9 43.1 - - - +
71D HIS* 1.3 74.1 - - - +
73D LYS* 1.3 59.9 + - - +
75D PHE* 3.7 7.0 - - - +
76D ARG* 2.8 40.3 + - + +
125D LEU* 3.9 25.8 - - + -
129D LEU* 5.6 2.4 - - + +
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Residues in contact with LYS 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 GLU* 3.2 20.6 + - + +
70D ALA* 3.2 8.0 + - - +
72D VAL* 1.3 78.7 - - - +
74D ARG* 1.3 61.4 + - + +
76D ARG* 3.3 6.7 + - + +
77D GLN* 2.9 58.4 + - + +
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ASP* 3.0 40.3 + - - -
36D PRO* 5.1 3.6 - - - +
37D VAL* 3.2 30.0 - - + +
70D ALA* 3.1 18.8 + - - +
71D HIS* 3.7 21.2 + - - +
73D LYS* 1.3 78.5 - - + +
75D PHE* 1.3 63.3 + - - +
77D GLN* 3.5 12.1 + - - +
78D ALA* 3.1 23.7 + - - +
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Residues in contact with PHE 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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15D LEU* 4.1 18.8 - - + -
36D PRO* 4.4 9.9 - - + -
37D VAL* 4.7 3.3 - - - +
40D VAL* 3.4 32.1 - - + -
51D VAL* 3.6 25.1 - - + -
53D PHE* 4.4 8.1 - + - -
58D LEU* 3.3 43.3 - - + -
71D HIS 3.2 6.9 + - - +
72D VAL* 3.7 4.7 - - - +
73D LYS 3.3 0.2 - - - -
74D ARG* 1.3 81.2 - - - +
76D ARG* 1.3 56.3 + - - +
78D ALA* 3.3 5.4 + - - +
79D LEU* 3.0 58.9 + - + +
86D VAL* 4.1 4.5 - - + -
129D LEU* 3.9 21.3 - - + -
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D VAL* 2.8 31.5 + - + +
73D LYS* 3.3 8.3 + - + +
75D PHE* 1.3 73.8 - - + +
77D GLN* 1.3 58.0 + - + +
79D LEU* 3.0 11.2 + - - +
80D ASP* 2.9 43.3 + - - +
128D GLU* 3.3 53.5 + - - +
129D LEU* 3.6 24.1 - - + +
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Residues in contact with GLN 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 LYS* 2.9 49.0 + - + +
74D ARG* 3.9 12.3 - - - +
76D ARG* 1.3 77.3 - - + +
78D ALA* 1.3 57.1 + - - +
80D ASP* 4.1 7.6 - - - +
81D ALA* 3.1 30.0 + - - +
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Residues in contact with ALA 78 (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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37D VAL* 3.8 30.3 - - + -
40D VAL* 3.6 19.1 - - + +
41D GLN* 5.3 3.4 - - + -
74D ARG 3.1 17.3 + - - +
75D PHE* 3.6 6.3 - - - +
76D ARG 3.1 0.2 - - - -
77D GLN* 1.3 73.7 - - - +
79D LEU* 1.3 62.8 + - - +
81D ALA* 4.3 2.6 - - - +
82D THR* 2.8 33.9 + - - +
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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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40D VAL* 4.1 7.6 - - + -
51D VAL* 4.2 8.7 - - + -
75D PHE* 3.0 59.5 + - + +
76D ARG* 3.0 10.3 + - + +
78D ALA* 1.3 76.3 - - - +
80D ASP* 1.3 61.9 + - - +
82D THR* 3.9 2.2 - - - -
83D GLY* 2.8 25.6 + - - -
84D MET* 3.2 42.7 + - + +
85D THR* 5.7 0.2 - - - -
86D VAL* 3.4 26.5 - - + -
129D LEU* 4.9 8.3 - - + -
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Residues in contact with ASP 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 ARG* 2.9 34.3 + - - +
77D GLN* 4.1 7.3 + - - +
79D LEU* 1.3 78.1 - - - +
81D ALA* 1.3 63.8 + - - +
82D THR 3.3 0.3 + - - -
83D GLY* 3.4 10.0 + - - -
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Residues in contact with ALA 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 GLN 3.1 19.5 + - - +
78D ALA* 4.3 4.0 - - - +
80D ASP* 1.3 78.2 - - - +
82D THR* 1.3 63.6 + - + +
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Residues in contact with THR 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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40D VAL* 3.7 9.6 - - + +
41D GLN* 4.3 25.6 - - + -
44D ALA* 4.0 20.3 - - + +
78D ALA* 2.8 24.7 + - - +
81D ALA* 1.3 80.7 - - + +
83D GLY* 1.3 63.5 + - - +
84D MET* 3.2 21.8 + - - +
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Residues in contact with GLY 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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49D TYR* 4.5 2.6 - - - +
79D LEU 2.8 10.7 + - - -
80D ASP* 3.4 8.7 + - - -
82D THR* 1.3 78.8 - - - +
84D MET* 1.3 64.1 + - - +
85D THR* 3.8 9.8 + - - +
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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