Contacts of the helix formed by residues 75 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.8 9.5 - - - +
17A GLU* 3.2 28.7 + - - +
20A ASP* 2.3 40.8 + - - +
73A PRO* 5.8 4.0 - - + -
74A GLY* 1.3 74.5 - - - +
76A PHE* 1.3 64.4 + - - +
77A ASP 3.4 2.5 - - - -
78A ALA* 3.2 41.5 + - + +
79A TYR* 3.3 20.1 + - - -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 6.0 1.3 - + - -
74A GLY 3.7 5.3 + - - +
75A ARG* 1.3 73.2 - - - +
77A ASP* 1.3 74.5 + - - +
79A TYR* 2.8 32.5 + + + +
80A LYS* 2.9 33.3 + - + -
102A LEU* 4.2 30.5 - - + -
841B RDG 5.0 12.8 - + - -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 3.4 0.6 - - - -
76A PHE* 1.3 93.1 - - - +
78A ALA* 1.3 56.7 + - - +
80A LYS* 3.1 9.0 + - - +
81A GLU* 2.9 32.5 + - - +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.1 12.4 - - + +
19A ARG* 4.8 1.4 + - - +
20A ASP* 4.8 1.1 - - - +
75A ARG* 3.2 53.5 + - + +
77A ASP* 1.3 77.6 - - - +
79A TYR* 1.3 60.9 + - - +
81A GLU* 3.2 29.1 - - - +
82A ALA* 3.9 8.7 + - - +
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Residues in contact with TYR 79 (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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12A PHE* 3.5 24.1 - + + -
13A PHE* 3.4 55.2 - + + +
16A VAL* 3.8 32.3 - - + -
17A GLU* 2.6 33.7 + - - +
31A ILE* 3.9 2.3 - - - +
74A GLY* 3.7 8.7 - - - -
75A ARG 3.3 32.1 + - - -
76A PHE* 2.8 19.8 + + + +
78A ALA* 1.3 82.3 - - + +
80A LYS* 1.3 57.7 - - - +
81A GLU 3.3 0.4 - - - -
82A ALA* 3.4 1.3 + - - -
83A SER* 2.9 29.0 + - - -
102A LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 80 (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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76A PHE* 2.9 31.4 + - + +
77A ASP* 3.1 15.0 + - - +
79A TYR* 1.3 76.0 - - - +
81A GLU* 1.3 61.5 + - - +
83A SER* 3.6 4.2 + - - -
84A ASN* 2.9 64.0 + - - +
87A ARG* 4.3 16.2 - - - +
102A LEU* 4.0 25.6 - - + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.9 22.1 + - - -
77A ASP 2.9 16.2 + - - +
78A ALA* 3.2 26.2 - - - +
80A LYS* 1.3 78.1 - - - +
82A ALA* 1.3 65.3 + - - +
84A ASN* 3.8 7.8 - - - +
85A HIS* 2.9 30.6 + - - +
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Residues in contact with ALA 82 (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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12A PHE* 4.2 17.7 - - + -
16A VAL* 4.9 6.7 - - + -
19A ARG* 5.3 2.0 - - - +
78A ALA 3.9 11.4 - - - +
79A TYR* 3.4 8.5 + - - +
80A LYS 3.3 0.4 - - - -
81A GLU* 1.3 86.3 - - + +
83A SER* 1.3 57.4 + - - +
85A HIS* 3.3 2.0 + - - +
86A ILE* 2.9 37.6 + - + +
134A LEU* 3.8 20.4 - - + -
136A LEU* 5.0 7.4 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.4 1.5 - - - -
79A TYR 2.9 18.3 + - - -
80A LYS* 3.6 6.1 + - - -
82A ALA* 1.3 75.5 - - - +
84A ASN* 1.3 65.4 + - - +
86A ILE* 3.1 8.4 - - - +
87A ARG* 3.0 43.1 + - - +
102A LEU* 2.9 53.4 + - - +
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Residues in contact with ASN 84 (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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80A LYS* 2.9 57.3 + - - +
81A GLU* 3.8 7.2 - - - +
83A SER* 1.3 75.5 + - - +
85A HIS* 1.3 64.1 + - - +
87A ARG* 3.3 14.2 + - - +
88A GLU* 2.9 22.5 + - - +
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Residues in contact with HIS 85 (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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81A GLU 2.9 19.4 + - - +
82A ALA* 3.5 4.9 - - - +
83A SER 3.2 0.2 - - - -
84A ASN* 1.3 75.3 - - - +
86A ILE* 1.3 58.0 + - - +
88A GLU* 2.9 22.1 + - - +
89A ILE* 2.9 25.4 + - + +
92A ARG* 4.4 0.2 + - - -
133A GLU* 2.8 53.8 + - + +
134A LEU* 3.3 27.2 - - + +
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Residues in contact with ILE 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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9A MET* 3.6 46.0 - - + -
12A PHE* 5.5 1.8 - - + -
82A ALA* 2.9 21.0 + - + +
83A SER* 3.1 20.6 - - - +
85A HIS* 1.3 72.9 - - - +
87A ARG* 1.3 58.6 + - + +
89A ILE* 3.3 10.2 + - - +
90A PHE* 2.9 52.0 + - + -
102A LEU 3.5 22.2 - - - +
103A ASP* 4.2 5.4 - - - -
104A GLU 5.1 0.2 - - - +
130A ILE* 4.1 13.0 - - + -
134A LEU* 3.6 19.7 - - + -
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Residues in contact with ARG 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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80A LYS* 4.3 16.5 - - - +
83A SER* 3.0 36.3 + - - +
84A ASN* 3.5 12.1 + - - +
86A ILE* 1.3 79.0 - - + +
88A GLU* 1.3 59.5 + - - +
90A PHE* 3.2 20.9 + - + +
91A SER* 2.9 27.2 + - - -
97A ILE* 4.2 5.6 - - + +
99A PRO* 3.4 36.5 - - + +
101A SER* 2.4 33.5 + - - +
102A LEU* 4.2 3.6 + - - +
104A GLU 5.3 1.6 + - - +
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Residues in contact with GLU 88 (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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84A ASN 2.9 11.5 + - - +
85A HIS* 2.9 31.5 + - - +
87A ARG* 1.3 71.9 - - - +
89A ILE* 1.3 64.6 + - - +
91A SER* 2.5 28.2 + - - +
92A ARG* 2.6 54.1 + - + +
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Residues in contact with ILE 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 HIS* 2.9 23.1 + - + +
86A ILE* 3.4 8.5 - - - +
88A GLU* 1.3 79.2 - - - +
90A PHE* 1.3 61.6 + - - +
92A ARG* 3.3 27.8 + - - +
93A TYR* 3.4 13.6 - - + -
126A ILE* 4.3 14.6 - - + -
129A THR* 4.0 24.2 - - + +
130A ILE* 3.7 31.2 - - + +
133A GLU* 3.8 15.5 - - - +
134A LEU* 3.6 30.1 - - + -
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Residues in contact with PHE 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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7A VAL* 3.5 30.7 - - + -
86A ILE* 2.9 45.2 + - + -
87A ARG* 3.4 19.5 - - + +
88A GLU 3.2 0.2 - - - -
89A ILE* 1.3 76.7 - - - +
91A SER* 1.3 57.3 + - - +
93A TYR* 3.0 20.4 + - - +
94A THR* 3.3 13.7 + - - +
97A ILE* 3.6 18.4 - - + +
103A ASP 6.0 0.2 - - - -
104A GLU* 5.1 1.1 - - - -
105A ALA* 3.5 32.8 - - + -
107A LEU* 4.1 19.1 - - + +
126A ILE* 3.5 33.4 - - + -
130A ILE* 3.9 8.5 - - + -
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Residues in contact with SER 91 (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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87A ARG 2.9 12.5 + - - -
88A GLU* 2.5 31.4 + - - +
90A PHE* 1.3 73.4 - - - +
92A ARG* 1.3 64.8 + - - +
93A TYR 3.2 0.7 + - - -
94A THR 3.3 21.4 + - - +
95A SER* 6.0 0.7 - - - -
97A ILE* 3.5 8.3 - - - +
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Residues in contact with ARG 92 (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 HIS* 4.4 0.2 + - - -
88A GLU* 2.6 49.1 + - + +
89A ILE* 3.3 20.9 - - - +
90A PHE 3.1 0.2 - - - -
91A SER* 1.3 78.4 + - - +
93A TYR* 1.3 67.5 + - + +
114A HIS* 3.3 18.5 + - - -
129A THR* 3.4 14.3 - - - +
133A GLU* 2.5 46.9 + - - -
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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
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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