Contacts of the helix formed by residues 72 - 92 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 5.3 11.0 - - - +
70B LEU 3.9 5.4 - - - +
71B LEU* 1.3 87.5 - - + +
73B GLY* 1.3 65.2 + - - +
74B GLU 3.5 1.1 - - - -
75B LEU* 3.0 20.8 + - + +
76B ALA 3.0 6.4 + - - -
175B GLU* 3.7 40.2 - - + +
178B SER* 3.7 13.5 - - - +
179B LEU* 4.3 18.4 - - + +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.6 2.4 + - - -
72B PRO* 1.3 69.7 - - - +
74B GLU* 1.3 57.2 + - - +
76B ALA* 3.2 7.6 + - - +
77B LYS* 3.0 34.7 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO 3.1 1.6 + - - -
73B GLY* 1.3 68.2 - - - +
75B LEU* 1.3 64.3 + - - +
76B ALA 3.0 1.6 - - - -
77B LYS* 2.4 37.8 + - - +
78B HIS* 2.8 46.8 + - + +
175B GLU* 3.1 25.4 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.0 6.4 - - + +
72B PRO* 3.0 16.0 + - + +
74B GLU* 1.3 79.6 - - - +
76B ALA* 1.3 61.0 + - - +
79B ALA* 3.1 25.5 + - - +
140B TYR* 3.6 36.8 - - + +
141B LEU* 3.7 11.2 - - + -
144B GLU* 4.4 13.0 - - + +
175B GLU* 3.1 40.3 + - + +
176B LEU* 4.0 26.7 - - + -
179B LEU* 4.2 18.6 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.4 8.2 - - + +
68B ARG* 4.5 16.2 - - + +
71B LEU* 3.8 29.3 - - + +
72B PRO 3.0 10.9 + - - +
73B GLY* 3.3 12.3 - - - +
74B GLU 3.0 0.2 - - - -
75B LEU* 1.3 75.7 - - - +
77B LYS* 1.3 66.3 + - + +
79B ALA* 3.3 2.3 + - - +
80B VAL* 2.9 30.7 + - - +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 5.2 12.6 - - - +
73B GLY 3.0 16.1 + - - +
74B GLU* 2.4 36.2 + - - +
76B ALA* 1.3 75.2 - - + +
78B HIS* 1.3 64.6 + - + +
80B VAL* 3.9 6.4 - - - +
81B SER* 3.2 27.0 + - - -
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU* 2.8 41.0 + - + +
76B ALA 3.2 0.8 - - - -
77B LYS* 1.3 82.6 - - + +
79B ALA* 1.3 64.4 + - - +
81B SER* 3.5 6.2 + - - -
82B GLU* 3.1 27.9 + - + +
140B TYR* 3.1 33.7 + + + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.4 2.5 - - + -
71B LEU* 4.2 11.2 - - + -
75B LEU 3.1 19.1 + - - +
76B ALA 3.7 2.7 - - - +
78B HIS* 1.3 74.5 - - - +
80B VAL* 1.3 60.7 + - - +
82B GLU* 2.9 5.7 + - - +
83B GLY 2.8 24.8 + - - -
137B ILE* 3.2 32.8 - - + +
140B TYR* 3.7 25.7 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 3.3 37.9 - - + +
67B VAL* 4.2 17.5 - - + -
68B ARG* 3.7 34.5 - - + +
76B ALA 2.9 20.9 + - - +
77B LYS* 3.9 5.4 - - - +
79B ALA* 1.3 74.9 - - - +
81B SER* 1.3 62.6 + - - +
83B GLY 3.2 0.9 + - - -
84B THR* 2.9 31.8 + - - +
133B TYR* 3.6 9.0 + - - +
137B ILE* 4.1 2.4 - - + +
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS 3.2 16.5 + - - -
78B HIS* 3.6 9.6 - - - -
80B VAL* 1.3 81.0 - - - +
82B GLU* 1.3 59.0 + - - +
84B THR* 3.4 6.1 + - - -
85B LYS* 2.9 29.6 + - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 3.1 14.0 + - + +
79B ALA 2.9 9.6 + - - +
81B SER* 1.3 76.6 + - - +
83B GLY* 1.3 64.2 + - - +
85B LYS* 3.7 33.2 - - - +
86B ALA* 3.0 25.6 + - - +
105B LEU* 6.1 0.5 - - - +
136B ALA* 3.5 18.7 - - + +
140B TYR* 4.2 23.2 - - + +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 2.8 13.4 + - - -
80B VAL 3.2 1.3 + - - -
82B GLU* 1.3 76.1 - - - +
84B THR* 1.3 60.8 + - - +
86B ALA* 3.3 3.5 + - - +
87B VAL* 3.1 28.1 + - - +
133B TYR* 3.4 28.5 - - - -
136B ALA* 3.7 14.3 - - - +
137B ILE* 4.2 3.8 - - - -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 4.1 8.0 + - - -
80B VAL* 2.9 19.9 + - - +
81B SER* 3.8 5.5 - - - -
83B GLY* 1.3 74.2 - - - +
85B LYS* 1.3 64.0 + - - +
87B VAL* 3.4 5.4 + - + +
88B THR* 3.0 37.3 + - - +
133B TYR* 3.5 11.1 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 2.9 19.4 + - - +
82B GLU* 3.7 35.7 - - - +
83B GLY 3.3 0.2 - - - -
84B THR* 1.3 75.9 - - - +
86B ALA* 1.3 60.2 + - - +
88B THR* 3.9 5.6 + - - +
89B LYS* 3.3 46.7 + - - +
103B ALA 5.4 2.0 + - - -
104B GLY 6.0 0.2 + - - -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLU 3.0 18.7 + - - +
83B GLY 3.7 1.8 - - - +
85B LYS* 1.3 76.6 - - - +
87B VAL* 1.3 60.8 + - - +
88B THR 3.2 1.3 - - - -
89B LYS* 3.2 2.6 + - - +
90B TYR* 2.9 29.1 + - - +
103B ALA* 3.9 20.5 - - - +
105B LEU* 4.2 9.0 - - + -
132B VAL* 3.8 14.0 - - + +
136B ALA* 3.6 20.6 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 4.9 4.0 - - - +
83B GLY 3.1 17.7 + - - +
84B THR* 4.0 5.8 - - + +
86B ALA* 1.3 74.1 - - - +
88B THR* 1.3 58.3 + - - +
90B TYR* 3.2 3.1 + - - +
91B THR* 2.9 33.8 + - - +
129B THR* 4.0 35.9 - - + +
132B VAL* 3.9 11.9 - - + -
133B TYR* 3.6 31.0 - - + -
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.0 26.1 + - - +
85B LYS* 3.9 7.6 - - - +
87B VAL* 1.3 77.5 - - - +
89B LYS* 1.3 64.2 + - - +
90B TYR 3.2 0.2 + - - -
91B THR* 3.2 5.4 + - - -
92B SER* 3.0 37.5 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS* 3.3 33.9 + - + +
86B ALA 3.2 5.7 + - - +
88B THR* 1.3 80.8 - - - +
90B TYR* 1.3 61.5 + - - +
92B SER* 3.8 4.5 + - - -
93B SER* 3.4 18.4 + - - -
101B GLN 5.9 0.4 - - - -
102B ARG 3.3 17.0 - - - +
103B ALA 4.0 18.4 - - - +
104B GLY* 4.4 15.8 + - - +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 2.9 13.1 + - - +
87B VAL* 3.2 11.2 - - - +
89B LYS* 1.3 74.5 - - - +
91B THR* 1.3 68.6 + - - +
93B SER* 3.3 9.0 + - - -
99B ARG* 2.4 64.5 + - + +
102B ARG* 3.3 71.4 + - + -
103B ALA* 4.1 3.8 - - + -
128B ALA* 4.2 9.9 - - + -
129B THR* 4.2 17.0 - - + -
132B VAL* 3.8 25.4 - - + -
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 2.9 27.9 + - - +
88B THR* 3.2 5.6 + - - -
90B TYR* 1.3 81.0 - - - +
92B SER* 1.3 62.2 + - - +
93B SER 3.0 11.1 + - - +
102B ARG* 5.2 1.8 + - - +
129B THR* 5.0 5.0 - - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 3.0 26.1 + - - +
89B LYS* 4.0 4.9 - - - -
90B TYR 3.4 0.2 - - - -
91B THR* 1.3 78.7 - - - +
93B SER* 1.3 60.1 + - - +
94B LYS* 5.2 4.0 - - - +
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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
------------------------------------------------------------
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