Contacts of the helix formed by residues 72 - 92 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU 3.9 5.4 - - - +
71A LEU* 1.3 87.8 - - + +
73A GLY* 1.3 67.3 + - - +
74A GLU 3.5 0.9 - - - -
75A LEU* 3.1 19.7 + - + +
76A ALA 3.1 5.5 + - - -
175A GLU* 3.6 40.8 - - + +
178A SER* 3.8 12.8 - - - +
179A LEU* 4.4 17.9 - - + +
54B LYS* 5.5 9.4 - - - +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 3.6 2.6 + - - -
72A PRO* 1.3 68.3 - - - +
74A GLU* 1.3 58.0 + - - +
76A ALA* 3.2 7.2 - - - +
77A LYS* 3.0 35.0 + - - +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO 3.1 2.0 + - - -
73A GLY* 1.3 68.6 - - - +
75A LEU* 1.3 65.8 + - - +
76A ALA 3.1 1.3 - - - -
77A LYS* 2.3 37.4 + - - +
78A HIS* 2.8 48.4 + - + +
175A GLU* 3.1 22.7 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.1 7.7 - - + +
72A PRO* 3.1 15.6 + - + +
74A GLU* 1.3 79.3 - - - +
76A ALA* 1.3 61.9 + - - +
79A ALA* 3.1 25.5 + - - +
140A TYR* 3.6 37.1 - - + +
141A LEU* 3.8 11.0 - - + -
144A GLU* 4.2 14.6 - - + +
175A GLU* 3.2 41.3 + - + +
176A LEU* 4.0 25.1 - - + -
179A LEU* 4.2 17.3 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.4 8.7 - - + +
68A ARG* 4.4 15.9 - - + +
71A LEU* 3.8 36.5 - - + +
72A PRO 3.1 2.4 + - - +
73A GLY* 3.2 12.3 - - - +
74A GLU 3.1 0.2 - - - -
75A LEU* 1.3 77.4 - - - +
77A LYS* 1.3 67.4 + - + +
79A ALA* 3.2 1.7 + - - +
80A VAL* 2.9 30.1 + - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 5.2 12.6 - - - +
73A GLY 3.0 16.1 + - - +
74A GLU* 2.3 36.7 + - - +
76A ALA* 1.3 75.6 - - + +
78A HIS* 1.3 64.6 + - + +
80A VAL* 3.9 5.8 - - - +
81A SER* 3.2 28.1 + - - -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 2.8 43.7 + - + +
77A LYS* 1.3 80.3 - - + +
79A ALA* 1.3 65.2 + - - +
81A SER* 3.5 6.6 + - - -
82A GLU* 3.1 27.2 + - - +
140A TYR* 3.1 34.0 + + + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.3 2.5 - - + -
71A LEU* 4.2 11.4 - - + -
75A LEU 3.1 19.3 + - - +
76A ALA 3.7 2.7 - - - +
78A HIS* 1.3 73.9 - - - +
80A VAL* 1.3 60.1 + - - +
82A GLU* 3.0 5.6 + - - +
83A GLY 2.9 25.1 + - - -
137A ILE* 3.2 33.7 - - + +
140A TYR* 3.7 24.7 - - + -
141A LEU* 5.1 0.2 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.5 37.0 - - + +
67A VAL* 4.1 17.7 - - + -
68A ARG* 3.7 35.7 - - + +
76A ALA 2.9 20.6 + - - +
77A LYS* 3.9 5.6 - - - +
79A ALA* 1.3 74.4 - - - +
81A SER* 1.3 62.4 + - - +
83A GLY 3.3 0.9 + - - +
84A THR* 2.9 32.4 + - - +
133A TYR* 3.6 10.2 + - - +
137A ILE* 4.2 2.2 - - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS 3.2 17.3 + - - -
78A HIS* 3.6 8.5 - - - -
79A ALA 3.2 0.2 - - - -
80A VAL* 1.3 80.8 - - - +
82A GLU* 1.3 60.2 + - - +
84A THR* 3.5 6.2 + - - -
85A LYS* 2.9 29.6 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS 3.1 14.6 + - - +
79A ALA 3.0 8.1 + - - +
81A SER* 1.3 77.3 + - - +
83A GLY* 1.3 66.3 + - - +
85A LYS* 3.6 33.7 + - - +
86A ALA* 3.0 25.3 + - - +
136A ALA* 3.5 18.7 - - + +
140A TYR* 4.2 22.1 - - + +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA 2.9 13.0 + - - -
80A VAL 3.3 1.7 + - - -
82A GLU* 1.3 76.8 - - - +
84A THR* 1.3 60.7 + - - +
86A ALA* 3.3 3.3 + - - +
87A VAL* 3.1 27.9 + - - +
133A TYR* 3.4 25.9 - - - -
136A ALA* 3.8 14.9 - - - +
137A ILE* 4.1 4.9 - - - -
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 4.2 8.1 + - - -
80A VAL* 2.9 19.9 + - - +
81A SER* 3.8 5.7 - - - -
83A GLY* 1.3 73.6 - - - +
85A LYS* 1.3 65.5 + - - +
87A VAL* 4.0 5.6 - - + +
88A THR* 3.1 35.9 + - - +
133A TYR* 3.5 11.0 - - + -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 2.9 18.6 + - - +
82A GLU* 3.6 36.3 + - - +
83A GLY 3.3 0.2 - - - -
84A THR* 1.3 76.9 - - - +
86A ALA* 1.3 61.3 + - - +
88A THR* 4.0 5.5 - - - +
89A LYS* 3.4 41.1 + - + +
103A ALA 5.5 1.6 + - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU 3.0 17.8 + - - +
83A GLY 3.6 2.0 - - - +
84A THR 3.1 0.4 - - - -
85A LYS* 1.3 77.9 - - - +
87A VAL* 1.3 60.3 + - - +
88A THR 3.2 1.3 - - - -
89A LYS* 3.3 2.9 + - - +
90A TYR* 2.9 29.3 + - - +
103A ALA* 3.9 21.2 - - - +
105A LEU* 4.3 7.9 - - + -
132A VAL* 3.8 14.1 - - + +
136A ALA* 3.6 20.9 - - + -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER* 4.9 4.7 - - - +
83A GLY 3.1 17.1 + - - +
84A THR* 4.0 5.8 - - + +
86A ALA* 1.3 74.8 - - - +
88A THR* 1.3 58.6 + - - +
90A TYR* 3.2 3.9 - - - +
91A THR* 2.9 34.2 + - - +
129A THR* 3.9 37.7 - - + +
132A VAL* 4.0 7.4 - - + -
133A TYR* 3.6 33.2 - - + +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.1 26.1 + - - +
85A LYS* 4.0 6.7 - - - +
87A VAL* 1.3 77.9 - - - +
89A LYS* 1.3 64.8 + - - +
90A TYR 3.2 0.2 + - - -
91A THR* 3.2 5.1 + - - -
92A SER* 3.0 39.2 + - - +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.4 31.9 + - + +
86A ALA 3.3 5.6 + - - +
88A THR* 1.3 80.8 - - - +
90A TYR* 1.3 60.7 + - - +
92A SER* 3.8 4.2 + - - -
93A SER* 3.3 18.7 + - - -
101A GLN 6.0 0.2 - - - -
102A ARG 3.3 18.9 - - - +
103A ALA 3.9 16.8 - - - +
104A GLY* 4.4 15.6 + - - -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 2.9 13.4 + - - +
87A VAL* 3.2 11.0 - - - +
88A THR 3.1 0.2 - - - -
89A LYS* 1.3 74.3 - - - +
91A THR* 1.3 69.3 + - - +
93A SER* 3.2 11.3 + - - -
99A ARG* 2.4 62.1 + - + +
102A ARG* 3.4 67.8 + - + -
103A ALA* 4.1 3.6 - - + -
128A ALA* 4.2 9.9 - - + -
129A THR* 4.2 16.8 - - + -
132A VAL* 3.8 26.9 - - + -
155C ASP* 5.5 4.3 - - - -
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 2.9 29.8 + - - +
88A THR* 3.8 5.6 - - - -
90A TYR* 1.3 77.5 - - - +
92A SER* 1.3 62.6 + - - +
93A SER 3.0 10.6 + - - +
102A ARG* 5.2 2.2 + - - +
129A THR* 5.0 4.5 - - - +
155C ASP* 6.0 1.8 - - - -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.0 26.7 + - - +
89A LYS* 3.9 4.7 - - - -
91A THR* 1.3 77.8 - - - +
93A SER* 1.3 58.4 + - - +
94A LYS* 5.0 4.7 - - - +
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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