Contacts of the helix formed by residues 87 - 104 (chain A) in PDB entry 1Q21
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 THR 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASN* 1.3 72.8 - - - +
88A LYS* 1.3 51.7 + - - +
90A PHE* 3.0 12.2 + - + +
91A GLU* 2.7 42.0 + - + +
124A THR* 2.7 41.6 + - - +
125A VAL* 3.6 14.8 - - + -
129A GLN* 5.3 4.7 - - - +
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 2.9 26.4 + - - -
86A ASN* 2.7 16.4 + - - +
87A THR* 1.3 73.9 - - - +
89A SER* 1.4 51.6 + - - +
91A GLU* 3.1 9.4 + - + +
92A ASP* 2.6 76.7 + - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.0 19.3 + - - +
14A VAL* 3.6 27.8 - - - -
81A VAL 5.0 0.7 - - - +
82A PHE* 3.7 5.3 - - - +
83A ALA 3.1 19.9 + - - -
86A ASN* 2.6 44.4 + - - +
88A LYS* 1.4 72.1 - - - +
90A PHE* 1.4 59.5 + - - +
92A ASP* 3.3 13.5 + - - +
93A ILE* 3.5 16.6 + - - +
96A TYR* 5.3 0.9 - - - -
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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
----------------------------------------------------------
82A PHE* 3.7 44.6 - + + -
86A ASN 3.8 0.9 - - - +
87A THR* 3.0 15.5 + - + +
89A SER* 1.4 78.4 + - - +
91A GLU* 1.3 79.7 + - + +
92A ASP 3.2 0.4 + - - -
93A ILE* 3.3 20.4 + - + +
113A LEU* 4.9 1.6 - - + -
125A VAL* 3.8 25.1 - - + -
129A GLN* 3.3 43.3 - - + -
130A ALA* 4.0 22.2 - - - -
133A LEU* 4.1 27.2 - - + +
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Residues in contact with GLU 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 THR* 2.7 27.3 + - + +
88A LYS* 3.1 10.5 + - + +
90A PHE* 1.3 91.1 - - + +
92A ASP* 1.4 62.9 + - - +
93A ILE 3.1 1.8 + - - -
94A HIS* 3.6 13.7 + - - +
95A GLN* 4.6 4.0 + - - +
129A GLN* 5.6 1.9 + - - -
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Residues in contact with ASP 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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11A ALA* 4.5 8.3 - - + +
64A TYR* 3.6 25.9 - - + -
88A LYS* 2.6 62.8 + - - +
89A SER* 3.3 11.0 + - - +
90A PHE 3.2 0.8 - - - -
91A GLU* 1.4 76.8 - - - +
93A ILE* 1.3 62.9 + - - +
94A HIS 3.2 0.4 - - - -
95A GLN* 3.1 22.0 + - - +
96A TYR* 3.2 29.0 + - + +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A CYS* 4.2 18.7 - - + -
81A VAL 4.0 19.3 - - - +
82A PHE* 4.1 7.2 - - + -
89A SER 3.5 13.0 + - - +
90A PHE* 3.4 25.4 - - + +
91A GLU 3.1 0.6 - - - -
92A ASP* 1.3 77.5 - - - +
94A HIS* 1.3 63.4 + - - +
96A TYR* 3.2 16.2 + - + +
97A ARG* 2.9 22.9 + - + +
113A LEU* 3.9 32.5 - - + -
133A LEU* 4.3 7.0 - - + -
137A TYR* 4.0 24.0 - - + +
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Residues in contact with HIS 94 (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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90A PHE 4.9 0.2 + - - -
91A GLU 3.6 8.0 + - - +
92A ASP 3.2 1.2 - - - -
93A ILE* 1.3 78.0 - - - +
95A GLN* 1.3 89.9 + - - +
97A ARG* 3.3 8.5 + - - +
98A GLU* 3.0 64.1 + - + +
137A TYR* 3.8 21.7 + - - +
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Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 4.0 36.4 - - + +
91A GLU 4.6 5.0 + - - +
92A ASP* 3.1 15.6 + - - +
94A HIS* 1.3 109.1 - - + +
96A TYR* 1.3 62.6 + - - +
98A GLU* 3.1 6.1 + - + +
99A GLN* 2.9 23.9 + - - +
102A ARG* 4.7 1.9 + - - -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 24.5 - - + -
10A GLY* 3.2 31.3 + - - -
11A ALA* 3.2 25.5 + - - +
62A GLU 5.6 0.2 + - - -
64A TYR* 3.8 29.5 - - + -
65A SER 3.9 13.9 - - - +
67A MET* 3.5 26.2 - - + +
80A CYS* 5.0 3.6 - - - -
89A SER 5.3 0.2 - - - -
92A ASP* 3.2 37.6 + - + -
93A ILE* 3.2 16.4 + - + +
95A GLN* 1.3 76.1 - - - +
97A ARG* 1.3 64.8 + - - +
99A GLN* 3.9 4.0 - - - +
100A ILE* 2.9 31.1 + - + +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A CYS* 5.3 2.8 - - - -
93A ILE* 2.9 17.8 + - + +
94A HIS* 3.7 10.7 + - - +
96A TYR* 1.3 79.2 - - - +
98A GLU* 1.4 82.8 + - - +
100A ILE* 3.7 9.8 - - - +
101A LYS* 2.8 53.9 + - + +
107A ASP* 2.8 37.0 + - - -
111A MET* 4.2 24.4 - - - +
137A TYR* 3.5 65.5 + - + +
139A ILE* 5.5 1.0 - - - +
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Residues in contact with GLU 98 (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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94A HIS* 3.0 58.8 + - + +
95A GLN* 3.1 5.8 + - + +
97A ARG* 1.4 106.7 + - - +
99A GLN* 1.3 61.1 + - - +
101A LYS* 2.6 28.2 + - - +
102A ARG* 2.7 47.5 + - - +
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Residues in contact with GLN 99 (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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62A GLU* 5.0 1.4 + - - -
65A SER* 3.2 53.4 + - - +
66A ALA* 3.3 25.0 - - + +
72A MET* 5.0 0.2 - - + -
95A GLN 2.9 14.0 + - - +
96A TYR 3.9 2.0 - - - +
98A GLU* 1.3 75.2 - - - +
100A ILE* 1.4 53.6 + - - +
102A ARG* 2.6 49.1 + - - +
103A VAL* 2.7 48.5 + - - +
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Residues in contact with ILE 100 (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 VAL* 4.2 13.0 - - + -
65A SER 5.4 0.9 - - - +
72A MET* 4.0 15.3 - - + -
78A PHE* 3.8 54.7 - - + -
80A CYS* 4.1 16.8 - - - -
96A TYR* 2.9 26.2 + - + +
97A ARG 3.7 2.9 - - - +
99A GLN* 1.4 73.5 - - - +
101A LYS* 1.3 61.0 + - - +
103A VAL* 3.7 8.3 - - - +
104A LYS* 2.9 32.1 + - - +
109A VAL* 3.8 9.0 - - + -
111A MET* 3.5 25.4 - - + -
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Residues in contact with LYS 101 (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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97A ARG* 2.8 54.9 + - + +
98A GLU* 2.6 39.5 + - - +
100A ILE* 1.3 74.2 - - - +
102A ARG* 1.4 57.7 + - - +
104A LYS* 4.6 0.2 - - - -
105A ASP* 2.9 26.5 + - - -
106A SER 3.2 31.6 + - - +
107A ASP* 2.9 39.2 + - - +
109A VAL* 4.6 5.8 - - + -
111A MET* 4.8 4.5 - - + -
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Residues in contact with ARG 102 (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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65A SER* 4.4 3.8 + - - -
95A GLN 4.7 2.0 + - - -
98A GLU* 2.7 44.0 + - - +
99A GLN* 2.6 51.4 + - - +
101A LYS* 1.4 72.7 - - - +
103A VAL* 1.3 66.8 + - + +
105A ASP* 3.3 13.9 + - - +
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Residues in contact with VAL 103 (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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66A ALA* 4.2 10.8 - - + -
69A ASP* 5.7 1.3 - - - +
72A MET* 4.3 32.1 - - + +
73A ARG* 4.0 41.5 + - - +
78A PHE* 5.7 0.4 - - + -
99A GLN* 2.7 39.0 + - - +
100A ILE* 3.7 14.1 - - + +
102A ARG* 1.3 76.3 - - + +
104A LYS* 1.3 64.1 + - + +
105A ASP* 3.2 6.7 + - - +
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Residues in contact with LYS 104 (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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72A MET 3.7 14.3 + - - +
73A ARG* 2.6 32.0 + - - +
74A THR* 3.7 2.2 + - - +
75A GLY 2.5 31.0 + - - -
76A GLU* 5.0 2.0 - - - +
78A PHE* 4.2 12.6 - - + -
100A ILE 2.9 19.2 + - - +
101A LYS 4.0 1.3 - - - +
103A VAL* 1.3 77.6 - - + +
105A ASP* 1.3 71.7 + - - +
106A SER* 3.2 9.4 + - - +
109A VAL* 4.0 29.8 - - + -
110A PRO* 6.4 0.4 - - - -
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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