Contacts of the helix formed by residues 71 - 88 (chain D) in PDB entry 3UF2
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 THR 71 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASP* 3.8 41.4 + - + -
25C SER* 5.7 0.7 - - - -
67D PHE* 4.1 3.5 - - - +
68D ARG* 2.7 34.7 + - + +
69D ASP 3.9 4.0 - - - +
70D ASN* 1.3 84.5 - - - +
72D PRO* 1.3 78.6 - - + -
73D ASN* 4.1 2.9 + - - +
74D ALA* 2.7 23.2 + - - +
75D ILE* 3.0 13.3 + - - +
105F THR* 4.9 0.2 - - - -
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Residues in contact with PRO 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG* 6.4 3.4 - - + -
24C ASP* 6.2 0.4 - - + -
25C SER* 6.5 0.4 - - - -
21D ARG* 3.5 45.3 + - - +
70D ASN 4.7 0.2 - - - +
71D THR* 1.3 86.7 - - + +
73D ASN* 1.3 60.2 + - - +
75D ILE* 3.5 7.2 + - + +
76D ALA* 2.9 27.3 + - - +
105F THR* 3.9 27.7 - - + +
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 3.0 34.8 + - - +
18D SER 4.9 0.9 - - - +
21D ARG* 4.5 8.3 + - - +
22D LEU* 3.5 28.3 + - + +
25D SER* 3.3 16.3 + - - -
26D GLN* 3.6 3.4 - - - +
67D PHE* 3.5 31.9 - - + -
71D THR* 3.1 3.8 + - - +
72D PRO* 1.3 82.4 - - - +
74D ALA* 1.3 67.0 + - - +
76D ALA* 3.2 8.3 + - - +
77D ILE* 3.1 27.4 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PHE* 3.7 23.0 - - + +
68D ARG 3.2 27.1 - - - +
69D ASP* 4.3 3.6 - - - +
70D ASN 4.1 6.3 - - - +
71D THR* 2.7 19.2 + - - +
73D ASN* 1.3 75.2 - - - +
75D ILE* 1.3 61.1 + - + +
77D ILE* 3.4 6.3 + - - +
78D VAL* 3.3 23.5 + - - +
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ASN* 4.6 11.9 - - - +
71D THR 3.0 15.2 + - - +
72D PRO 3.9 6.5 - - - +
74D ALA* 1.3 74.1 - - + +
76D ALA* 1.3 66.1 + - - +
78D VAL* 2.9 11.0 + - + +
79D GLN* 2.9 27.6 + - + +
34F THR* 3.8 24.7 - - + -
105F THR* 3.5 43.3 - - + +
106F PHE 4.3 1.1 - - - +
107F TYR* 3.8 38.8 - - + -
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D SER* 4.2 27.8 + - - +
22D LEU* 4.6 10.8 - - + -
72D PRO 2.9 16.4 + - - +
73D ASN* 3.2 16.8 + - - +
75D ILE* 1.3 76.9 - - - +
77D ILE* 1.3 61.2 + - - +
79D GLN* 3.4 16.3 + - - +
80D LEU* 3.1 30.5 + - + +
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Residues in contact with ILE 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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22D LEU* 3.5 17.3 - - + -
61D MET* 3.9 28.7 - - + +
65D MET* 3.5 48.5 - - + +
67D PHE* 4.1 7.2 - - + -
73D ASN 3.1 13.9 + - - +
74D ALA* 3.6 7.6 - - - +
75D ILE 3.1 0.4 - - - -
76D ALA* 1.3 74.8 - - - +
78D VAL* 1.3 61.0 + - + +
80D LEU* 3.0 14.5 + - + +
81D GLN* 2.8 45.4 + - + +
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Residues in contact with VAL 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ALA 3.5 13.9 - - - +
75D ILE* 2.9 14.5 + - + +
77D ILE* 1.3 77.0 - - + +
79D GLN* 1.3 63.0 + - - +
81D GLN* 3.2 15.5 + - - +
82D GLU* 2.9 43.1 + - + +
107F TYR* 4.1 16.2 - - + -
85I LEU* 4.4 24.5 - - + +
86I ARG* 5.5 1.6 - - - -
88I LYS* 6.5 0.7 - - + -
89I SER* 5.4 7.4 - - - +
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLY 5.6 0.5 - - - +
15D HIS* 4.6 16.1 + - + +
18D SER* 4.4 11.8 + - - -
75D ILE* 2.9 18.7 + - + +
76D ALA* 3.4 16.1 - - - +
78D VAL* 1.3 77.9 - - - +
80D LEU* 1.3 57.3 + - + +
82D GLU* 3.2 13.7 + - - +
83D LEU* 2.9 27.1 + - - +
107E TYR* 5.2 0.7 + - - -
33F ILE* 5.8 0.2 - - - +
34F THR* 3.1 36.2 + - - +
107F TYR* 3.8 24.0 - - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS* 3.8 41.5 - - + +
18D SER* 5.1 4.3 - - - +
19D LEU* 4.4 30.7 - - + -
22D LEU* 5.7 0.7 - - + -
61D MET* 4.0 19.3 - - - -
65D MET* 5.5 2.2 - - + -
76D ALA* 3.1 23.2 + - + +
77D ILE* 3.0 22.1 + - + +
79D GLN* 1.3 77.5 - - + +
81D GLN* 1.3 52.4 + - - +
83D LEU* 3.3 15.8 + - + +
84D SER* 2.8 37.0 + - - -
117D VAL* 6.2 0.2 - - + -
121D PHE* 4.8 12.5 - - + -
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Residues in contact with GLN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLN* 5.0 3.6 + - - +
61D MET* 4.3 15.6 + - + +
62D GLU* 3.0 43.5 + - - +
77D ILE* 2.8 34.5 + - + +
78D VAL* 3.6 15.9 - - - +
80D LEU* 1.3 73.9 - - - +
82D GLU* 1.3 65.4 + - - +
84D SER* 3.2 16.1 + - - -
85D LEU* 3.3 13.5 + - - +
85I LEU* 3.6 34.4 - - + +
88I LYS* 5.9 2.6 - - - +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D VAL* 2.9 26.0 + - + +
79D GLN* 3.4 9.3 - - - +
81D GLN* 1.3 75.9 - - - +
83D LEU* 1.3 61.9 + - - +
84D SER 3.4 0.2 + - - -
85D LEU* 3.5 17.4 + - - +
86D ARG 3.9 3.1 + - - -
107E TYR* 3.9 24.2 + - - +
32F GLN* 4.7 0.2 - - - +
107F TYR* 2.7 39.3 + - - -
82I GLU* 3.8 27.8 - - + +
85I LEU* 3.7 20.0 - - + +
86I ARG* 3.9 18.9 - - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D MET* 3.4 42.4 - - + +
11D ILE* 4.3 14.4 - - + +
15D HIS* 3.7 40.6 - - + +
79D GLN 2.9 13.2 + - - +
80D LEU* 3.4 16.8 - - + +
82D GLU* 1.3 76.7 - - - +
84D SER* 1.3 62.1 + - - +
86D ARG* 3.4 4.7 + - - +
87D LEU* 3.2 28.1 + - + +
121D PHE* 4.3 15.0 - - + -
107E TYR* 4.3 13.6 + - + -
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Residues in contact with SER 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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54D PHE* 3.9 9.2 - - - -
58D GLN* 3.2 40.2 + - - -
61D MET* 3.5 8.0 - - - +
80D LEU 2.8 20.6 + - - -
81D GLN* 3.5 8.3 - - - -
82D GLU 3.2 0.4 - - - -
83D LEU* 1.3 77.3 - - - +
85D LEU* 1.3 64.4 + - - +
87D LEU* 3.1 11.6 + - - +
88D LYS* 3.1 23.8 + - - +
121D PHE* 4.2 6.9 - - - -
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Residues in contact with LEU 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 GLN 3.3 8.8 + - - +
82D GLU 3.7 7.6 - - - +
84D SER* 1.3 79.5 - - - +
86D ARG* 1.3 61.8 + - - +
88D LYS* 3.6 23.4 + - + +
89D SER* 4.4 1.9 + - - -
62I GLU* 4.8 7.2 - - - +
78I VAL* 4.4 23.2 - - + +
81I GLN* 3.8 38.4 - - + +
82I GLU* 3.6 44.9 - - + +
85I LEU* 3.7 17.5 - - + -
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Residues in contact with ARG 86 (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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10D MET* 3.4 25.2 - - + +
82D GLU 3.9 3.2 + - - +
83D LEU 3.4 6.6 + - - +
84D SER 3.2 0.4 - - - -
85D LEU* 1.3 76.3 - - - +
87D LEU* 1.3 63.0 + - - +
88D LYS 3.1 0.4 - - - -
89D SER* 2.5 33.2 + - - +
90D CYS* 4.4 0.2 - - - -
34E THR* 5.9 0.7 - - - +
105E THR* 6.3 2.7 - - + -
107E TYR* 3.9 28.9 - - + -
78I VAL* 6.1 1.8 - - - -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D MET* 4.3 8.7 - - + -
11D ILE* 3.8 28.0 - - + -
54D PHE* 3.5 36.6 - - + -
83D LEU* 3.2 29.3 + - + +
84D SER* 3.1 5.0 + - - +
86D ARG* 1.3 74.3 - - - +
88D LYS* 1.3 54.2 + - - +
89D SER 3.0 5.6 - - - -
90D CYS* 2.7 44.0 + - + +
91D PHE* 3.2 15.0 - - + -
121D PHE* 4.5 4.3 - - + -
124D THR* 5.0 1.6 - - + -
128D LEU* 3.5 32.1 - - + -
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 4.0 14.4 - - + -
55D LEU* 6.4 1.1 - - + -
58D GLN* 4.3 30.4 + - - +
84D SER* 3.1 21.3 + - - +
85D LEU* 3.7 21.1 - - + +
86D ARG 3.1 1.2 - - - -
87D LEU* 1.3 75.8 - - - +
89D SER* 1.3 55.1 + - - +
90D CYS 3.2 0.9 - - - -
91D PHE* 3.2 26.0 - - - +
62I GLU* 2.8 36.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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