Contacts of the helix formed by residues 75 - 94 (chain F) in PDB entry 4Q44
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 ARG 75 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F VAL* 3.6 18.2 + - - +
17F GLU* 3.1 28.9 + - - +
20F ASP* 2.3 39.3 + - - +
73F PRO* 5.7 3.8 - - + -
74F GLY* 1.3 77.2 - - - +
76F PHE* 1.3 65.7 + - - +
77F ASP 3.3 2.5 - - - -
78F ALA* 3.1 29.9 + - + +
79F TYR* 3.1 19.2 + - - -
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Residues in contact with PHE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F PHE* 6.2 1.1 - + - -
74F GLY 3.8 2.8 + - - -
75F ARG* 1.3 73.8 - - - +
77F ASP* 1.3 83.1 + - - +
79F TYR* 2.9 31.9 + + + +
80F LYS* 2.9 39.0 + - + -
102F LEU* 4.0 28.7 - - + -
841G RDG 6.4 2.2 - + - -
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Residues in contact with ASP 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ARG 3.2 1.2 + - - -
76F PHE* 1.3 104.0 - - - +
78F ALA* 1.3 56.6 + - - +
80F LYS* 3.7 5.8 - - - +
81F GLU* 2.9 27.9 + - - +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F VAL* 4.1 20.6 - - + +
19F ARG* 5.0 6.0 + - - +
20F ASP* 4.9 1.3 - - - +
75F ARG* 3.1 38.4 + - + +
77F ASP* 1.3 77.0 - - - +
79F TYR* 1.3 59.4 + - - +
81F GLU* 3.3 8.5 + - - +
82F ALA* 2.9 28.2 + - - +
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Residues in contact with TYR 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 3.2 30.0 - - + -
13F PHE* 3.5 48.7 - + + -
16F VAL* 3.8 34.8 - - + -
17F GLU* 2.5 35.5 + - - +
31F ILE* 3.8 5.5 - - - +
74F GLY* 3.5 10.3 - - - -
75F ARG 3.1 33.7 + - - -
76F PHE* 2.9 16.5 + + + +
78F ALA* 1.3 75.9 - - + +
80F LYS* 1.3 56.6 + - - +
82F ALA* 3.5 1.5 + - - -
83F SER* 2.9 25.6 + - - -
102F LEU* 3.8 9.9 - - + -
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Residues in contact with LYS 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F PHE* 2.9 40.0 + - + +
77F ASP* 3.7 7.6 - - - +
78F ALA 3.2 0.2 - - - -
79F TYR* 1.3 76.0 - - - +
81F GLU* 1.3 59.5 + - - +
83F SER* 4.1 3.1 + - - -
84F ASN* 2.9 63.7 + - - +
87F ARG* 4.0 17.6 - - - +
102F LEU* 3.8 24.4 - - + +
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ARG* 6.2 1.8 - - - +
77F ASP 2.9 18.1 + - - +
78F ALA* 3.3 9.6 + - - +
80F LYS* 1.3 77.2 - - - +
82F ALA* 1.3 63.6 + - - +
84F ASN* 3.4 8.8 + - - +
85F HIS* 3.0 35.8 + - + +
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Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F MET* 6.1 0.2 - - + -
12F PHE* 3.8 22.0 - - + -
16F VAL* 4.5 8.3 - - + -
19F ARG* 5.2 3.6 - - - +
78F ALA 2.9 17.0 + - - +
79F TYR* 3.6 5.6 - - - +
81F GLU* 1.3 79.0 - - - +
83F SER* 1.3 57.3 + - - +
85F HIS* 3.1 3.9 + - - +
86F ILE* 2.9 34.9 + - + +
134F LEU* 3.6 22.0 - - + -
136F LEU* 4.6 4.7 - - + -
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Residues in contact with SER 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 4.3 1.3 - - - -
79F TYR 2.9 19.6 + - - -
80F LYS* 3.6 6.2 - - - +
81F GLU 3.3 0.2 - - - -
82F ALA* 1.3 76.2 - - - +
84F ASN* 1.3 56.7 + - - +
86F ILE* 3.1 9.9 - - - +
87F ARG* 2.9 46.8 + - - +
102F LEU* 2.6 53.8 + - - +
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Residues in contact with ASN 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LYS* 2.9 55.9 + - - +
81F GLU* 3.8 8.7 + - - +
83F SER* 1.3 75.7 - - - +
85F HIS* 1.3 58.1 + - - +
87F ARG* 3.8 13.5 + - - +
88F GLU* 2.9 30.0 + - - +
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Residues in contact with HIS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLU* 3.0 25.8 + - + +
82F ALA 3.1 9.4 + - - +
84F ASN* 1.3 77.3 - - - +
86F ILE* 1.3 56.7 + - - +
88F GLU* 3.2 19.1 + - - +
89F ILE* 2.9 25.1 + - + +
92F ARG* 4.6 0.2 + - - -
133F GLU* 2.8 48.8 + - + +
134F LEU* 3.6 29.8 - - + +
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Residues in contact with ILE 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 5.7 0.2 - - + -
9F MET* 3.9 33.2 - - + -
12F PHE* 5.9 0.9 - - + -
82F ALA* 2.9 14.6 + - + +
83F SER* 3.1 18.8 - - - +
85F HIS* 1.3 74.7 - - - +
87F ARG* 1.3 58.5 + - + +
89F ILE* 3.2 10.1 + - - +
90F PHE* 2.9 50.7 + - + -
102F LEU 3.7 20.0 - - - +
103F ASP 3.8 18.2 - - - +
130F ILE* 4.2 13.5 - - + -
134F LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LYS* 4.0 19.6 - - - +
83F SER* 2.9 35.5 + - - +
84F ASN* 3.8 11.9 + - - +
86F ILE* 1.3 79.0 - - + +
88F GLU* 1.3 60.6 + - - +
90F PHE* 3.2 19.2 + - + +
91F SER* 2.9 27.5 + - - -
97F ILE* 4.1 7.5 - - + +
99F PRO* 3.4 37.2 - - + +
101F SER* 2.6 34.5 + - - +
102F LEU* 4.2 5.1 + - - +
104F GLU 5.4 0.8 + - - -
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Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASN 2.9 15.4 + - - +
85F HIS* 3.3 21.8 + - - +
87F ARG* 1.3 76.5 - - - +
89F ILE* 1.3 58.3 + - - +
91F SER* 2.3 30.8 + - - +
92F ARG* 3.0 47.6 + - - +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F HIS* 2.9 16.4 + - + +
86F ILE* 3.3 9.0 - - - +
87F ARG 3.1 0.2 - - - -
88F GLU* 1.3 74.8 - - - +
90F PHE* 1.3 65.9 + - + +
92F ARG* 3.2 43.3 + - - +
93F TYR* 3.5 11.9 - - + -
126F ILE* 4.2 25.8 - - + +
129F THR* 3.2 42.2 - - + +
130F ILE* 3.9 10.8 - - + -
133F GLU* 3.8 6.5 - - - +
134F LEU* 3.6 24.7 - - + -
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Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 3.6 32.1 - - + -
86F ILE* 2.9 44.1 + - + -
87F ARG* 3.2 17.7 + - + +
89F ILE* 1.3 76.5 - - - +
91F SER* 1.3 63.4 + - - +
93F TYR* 3.1 16.3 + - - +
94F THR* 3.1 15.9 + - - +
97F ILE* 3.6 22.1 - - + +
103F ASP 5.4 0.2 - - - -
105F ALA* 3.5 32.5 - - + -
107F LEU* 3.9 20.6 - - + +
126F ILE* 3.4 32.5 - - + -
130F ILE* 4.1 4.9 - - + -
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ARG 2.9 12.4 + - - -
88F GLU* 2.3 34.8 + - - +
90F PHE* 1.3 77.6 - - - +
92F ARG* 1.3 62.0 + - - +
93F TYR 3.3 0.7 + - - -
94F THR 3.3 19.5 + - - +
95F SER* 5.3 0.8 - - - +
97F ILE* 3.6 7.1 - - - +
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Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F HIS* 4.6 0.2 + - - -
88F GLU* 3.0 45.4 + - - +
89F ILE* 3.4 23.0 - - - +
90F PHE 3.1 0.6 - - - -
91F SER* 1.3 78.6 - - - +
93F TYR* 1.3 70.4 + - + +
114F HIS* 2.9 21.1 + - + -
129F THR* 3.6 16.2 - - - +
133F GLU* 2.9 40.8 + - - -
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Residues in contact with TYR 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 3.5 23.8 - - + -
90F PHE 3.1 6.1 + - - +
91F SER 4.3 0.2 - - - -
92F ARG* 1.3 91.0 - - + +
94F THR* 1.3 64.8 + - + +
107F LEU* 5.0 1.1 - - + -
109F VAL* 4.9 2.8 - - + +
112F SER* 4.2 8.7 + - - +
114F HIS* 3.2 51.7 + + + -
115F CYS* 4.9 0.7 - - - -
122F ILE* 3.8 32.5 - - + -
125F GLU* 3.1 52.6 + - + +
126F ILE* 4.0 22.2 - - + -
129F THR* 5.0 4.6 + - + +
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Residues in contact with THR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F PHE 3.1 14.5 + - - +
91F SER* 3.3 13.0 + - - +
93F TYR* 1.3 80.5 - - - +
95F SER* 1.3 66.1 + - - +
96F ARG* 2.9 34.2 + - - +
97F ILE* 3.4 11.9 - - + +
107F LEU* 3.8 37.2 - - + -
108F ASP 3.4 9.9 + - - +
109F VAL* 4.3 10.1 - - + -
112F SER* 6.2 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
------------------------------------------------------------
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