Contacts of the helix formed by residues 72 - 92 (chain D) in PDB entry 4NFT
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 PRO 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU 4.0 4.0 - - - +
71D LEU* 1.3 90.5 - - + +
73D GLY* 1.3 65.1 + - - +
74D GLU 3.5 1.1 - - - -
75D LEU* 3.2 21.2 + - + +
76D ALA 3.2 6.1 + - - -
175D GLU* 3.5 50.0 - - + +
178D SER* 3.7 20.9 - - - +
179D LEU* 4.4 8.7 - - - +
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Residues in contact with GLY 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LEU 3.6 3.1 + - - -
72D PRO* 1.3 68.0 - - - +
74D GLU* 1.3 61.6 + - - +
76D ALA* 3.2 21.2 + - - +
77D LYS* 3.4 23.4 + - - -
175D GLU* 4.7 0.2 + - - -
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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
----------------------------------------------------------
72D PRO 3.5 0.6 - - - -
73D GLY* 1.3 71.0 - - - +
75D LEU* 1.3 66.1 + - - +
76D ALA 3.3 0.3 + - - -
77D LYS* 3.2 35.1 + - - +
78D HIS* 3.3 39.2 + - + +
175D GLU* 3.4 16.3 + - - +
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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
----------------------------------------------------------
71D LEU* 4.0 20.0 - - + -
72D PRO* 3.2 16.4 + - + +
74D GLU* 1.3 75.7 - - - +
76D ALA* 1.3 63.8 + - - +
78D HIS* 3.3 6.8 + - - +
79D ALA* 3.0 19.6 + - - +
140D TYR* 3.8 19.5 - - + +
141D LEU* 3.8 26.5 - - + -
144D GLU* 5.8 5.2 - - + -
175D GLU* 3.1 31.7 + - + +
176D LEU* 4.3 14.1 - - + -
179D LEU* 4.2 22.0 - - + -
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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
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67D VAL* 4.3 15.3 - - + +
68D ARG* 4.5 18.4 - - + -
71D LEU* 4.1 24.8 - - + +
72D PRO 3.2 7.8 + - - +
73D GLY* 3.3 12.6 - - - +
74D GLU 3.2 0.8 - - - -
75D LEU* 1.3 79.3 - - - +
77D LYS* 1.3 59.9 + - + +
79D ALA* 3.1 3.2 + - - +
80D VAL* 2.9 33.7 + - + +
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ARG* 5.3 17.6 - - - +
73D GLY* 3.4 20.7 + - - +
74D GLU* 3.2 31.6 + - - +
75D LEU 3.3 0.6 - - - -
76D ALA* 1.3 78.9 - - + +
78D HIS* 1.3 55.2 + - + +
80D VAL* 3.9 5.6 - - - +
81D SER* 2.7 39.7 + - - +
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Residues in contact with HIS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLU* 3.3 29.8 + - + -
75D LEU* 3.3 10.3 + - - +
76D ALA 3.2 0.2 - - - -
77D LYS* 1.3 79.3 - - + +
79D ALA* 1.3 62.1 + - - +
81D SER* 3.4 7.2 + - - -
82D GLU* 3.1 27.4 + - - +
140D TYR* 3.3 27.6 + - + +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 4.8 1.6 - - + -
71D LEU* 4.2 14.1 - - + -
75D LEU 3.0 12.6 + - - +
76D ALA* 3.5 8.1 - - - +
78D HIS* 1.3 77.3 - - - +
80D VAL* 1.3 57.0 - - - +
82D GLU* 3.2 5.4 + - - +
83D GLY 3.0 20.3 + - - -
137D ILE* 3.4 35.2 - - + +
140D TYR* 3.9 24.6 - - + -
141D LEU* 5.0 1.1 - - + -
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Residues in contact with VAL 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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64D GLN* 3.8 45.5 - - + +
67D VAL* 4.5 11.7 - - + -
68D ARG* 5.7 2.0 - - + -
76D ALA* 2.9 20.1 + - + +
77D LYS* 4.1 6.1 - - - +
79D ALA* 1.3 73.0 - - - +
81D SER* 1.3 61.8 + - - +
83D GLY* 3.0 3.8 + - - +
84D THR* 2.8 30.9 + - - +
133D TYR* 3.6 13.2 - - + -
137D ILE* 4.3 18.4 - - + -
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Residues in contact with SER 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LYS* 2.7 23.3 + - - +
78D HIS* 3.7 8.4 - - - -
80D VAL* 1.3 78.2 - - - +
82D GLU* 1.3 58.4 + - - +
84D THR* 3.4 8.1 + - - +
85D LYS* 2.9 43.3 + - - +
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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
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78D HIS 3.1 17.6 + - - +
79D ALA 3.6 8.3 - - - +
80D VAL 3.2 0.2 - - - -
81D SER* 1.3 74.7 - - - +
83D GLY* 1.3 66.7 + - - +
85D LYS* 3.5 34.0 + - - +
86D ALA* 3.1 22.5 + - - +
136D ALA* 3.6 10.3 - - + +
140D TYR* 3.5 39.9 - - + +
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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
----------------------------------------------------------
79D ALA 3.0 10.2 + - - -
80D VAL* 3.0 9.1 + - - -
82D GLU* 1.3 76.6 - - - +
84D THR* 1.3 62.7 + - - +
86D ALA* 3.1 5.9 + - - +
87D VAL* 3.0 24.3 + - - +
133D TYR* 3.5 26.0 - - - -
136D ALA* 3.7 15.2 - - - +
137D ILE* 4.8 0.4 - - - -
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 2.8 18.2 + - - +
81D SER* 3.7 10.5 - - - -
82D GLU 3.3 0.2 - - - -
83D GLY* 1.3 74.9 - - - +
85D LYS* 1.3 62.9 + - + +
87D VAL* 3.1 4.8 + - + +
88D THR* 2.9 34.0 + - - +
133D TYR* 2.4 29.9 + - - +
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Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER* 2.9 30.8 + - - +
82D GLU* 3.5 30.7 + - - +
84D THR* 1.3 76.1 - - + +
86D ALA* 1.3 62.7 + - - +
88D THR* 3.3 9.6 + - - -
89D LYS* 3.0 43.5 + - - +
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Residues in contact with ALA 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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82D GLU 3.1 12.9 + - - +
83D GLY 3.1 10.1 + - - +
85D LYS* 1.3 78.0 - - - +
87D VAL* 1.3 51.2 + - - +
89D LYS* 3.3 7.6 + - - +
90D TYR* 2.7 34.1 + - - +
103D ALA* 3.7 21.9 - - - +
105D LEU* 4.3 8.1 - - + -
132D VAL* 3.8 16.4 - - + -
136D ALA* 3.8 14.6 - - + -
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Residues in contact with VAL 87 (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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83D GLY 3.0 9.6 + - - +
84D THR* 3.7 7.9 - - + +
86D ALA* 1.3 72.5 - - - +
88D THR* 1.3 60.7 + - - +
90D TYR* 3.2 7.5 - - + +
91D THR* 2.8 39.3 + - + +
129D THR* 3.6 28.7 - - + -
132D VAL* 3.7 20.9 - - + -
133D TYR* 3.4 38.1 - - + -
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Residues in contact with THR 88 (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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84D THR* 2.9 22.5 + - - +
85D LYS* 3.3 13.1 - - - +
87D VAL* 1.3 77.1 - - - +
89D LYS* 1.3 67.8 + - + +
91D THR* 3.2 17.1 + - - -
92D SER* 3.3 16.0 + - - +
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Residues in contact with LYS 89 (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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85D LYS* 3.0 38.5 + - - +
86D ALA* 3.5 7.6 - - - +
88D THR* 1.3 77.7 - - + +
90D TYR* 1.3 64.0 + - - +
92D SER* 3.0 25.4 + - - +
93D SER* 3.9 2.1 + - - -
102D ARG 3.6 16.2 - - - +
103D ALA 3.9 17.3 - - - +
104D GLY* 4.9 5.2 - - - -
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Residues in contact with TYR 90 (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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86D ALA 2.7 19.0 + - - +
87D VAL* 3.2 13.0 - - - +
89D LYS* 1.3 72.7 - - - +
91D THR* 1.3 70.3 + - + +
92D SER 3.0 13.2 - - - +
99D ARG* 2.9 67.4 + - + -
102D ARG* 3.2 66.1 + - + +
103D ALA* 4.0 6.5 - - + -
128D ALA* 4.7 10.5 - - + -
129D THR* 5.0 8.1 - - + -
132D VAL* 3.8 25.1 - - + -
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Residues in contact with THR 91 (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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87D VAL* 2.8 29.4 + - + +
88D THR* 3.2 10.7 + - - -
90D TYR* 1.3 85.3 - - + +
92D SER* 1.3 57.1 + - - +
102D ARG* 5.3 0.4 - - - +
129D THR* 4.9 7.4 - - + -
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D THR* 3.3 12.7 + - - +
89D LYS* 3.0 17.4 + - - +
90D TYR 3.0 7.4 - - - +
91D THR* 1.3 77.4 + - - +
93D SER* 1.3 83.2 + - - +
102D ARG* 4.8 0.2 + - - -
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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
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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