Contacts of the helix formed by residues 93 - 112 (chain A) in PDB entry 3C9T
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 GLU 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ARG* 3.8 16.5 + - - -
91A ASP 3.3 3.7 + - - +
92A LEU* 1.3 91.0 - - - +
94A VAL* 1.3 56.7 + - - +
95A SER* 3.8 18.6 - - - +
96A TYR* 2.8 42.7 + - + +
97A VAL* 3.6 3.1 + - - +
0B THR* 4.5 14.4 - - + +
1B MET 3.5 12.8 - - - +
2B ARG* 4.0 25.9 + - - +
3B LEU* 4.9 0.2 - - - -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 3.6 1.2 + - - -
93A GLU* 1.3 70.8 - - - +
95A SER* 1.3 63.1 + - - +
96A TYR 3.2 0.2 + - - -
97A VAL* 3.2 5.2 + - + +
98A GLU* 3.0 22.8 + - + +
1B MET* 3.0 46.1 + - + +
2B ARG 3.6 21.1 - - - +
3B LEU* 4.1 10.1 - - + -
6B LEU* 3.8 31.2 - - + -
14B LEU* 4.7 16.3 - - + +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.8 16.9 - - - +
94A VAL* 1.3 79.5 - - - +
96A TYR* 1.3 59.0 + - - +
98A GLU* 3.7 12.5 - - - +
99A ARG* 2.9 45.7 + - - +
0B THR* 4.5 9.8 + - - +
1B MET 4.7 0.4 + - - -
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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
----------------------------------------------------------
51A PHE* 3.7 25.5 - - - -
52A LEU 4.3 1.4 + - - -
53A ARG* 3.5 29.5 + - + -
55A TYR 4.3 5.3 + - - -
57A PRO* 3.7 35.4 - - + +
60A VAL* 4.4 11.1 - - + +
88A LEU* 6.3 0.2 - - + -
92A LEU* 3.8 31.2 - - + -
93A GLU* 2.8 27.7 + - + +
95A SER* 1.3 81.6 + - - +
97A VAL* 1.3 58.3 + - + +
100A PHE* 2.9 42.0 + + + +
126A ILE* 3.7 25.1 - - + +
128A ILE* 6.0 0.4 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 5.0 5.8 - - + -
88A LEU* 4.4 9.4 - - + -
92A LEU* 3.8 24.5 - - + -
93A GLU 4.3 2.0 - - - +
94A VAL* 3.2 6.1 + - + +
96A TYR* 1.3 77.4 - - + +
98A GLU* 1.3 57.4 + - - +
100A PHE* 3.5 5.8 + - + +
101A TYR* 3.0 49.9 + - + -
3B LEU* 4.1 27.6 - - + -
11B LEU* 4.0 22.2 - - + -
14B LEU* 4.5 8.7 - - + -
15B ILE* 4.6 0.7 - - + -
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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
----------------------------------------------------------
94A VAL* 3.0 19.4 + - + +
95A SER* 3.7 12.1 - - - +
97A VAL* 1.3 77.6 - - - +
99A ARG* 1.3 64.5 + - + +
101A TYR* 3.3 4.8 + - - +
102A ILE* 3.2 36.7 + - + +
14B LEU* 3.8 29.4 - - + +
17B LYS* 5.7 2.6 + - - -
18B THR* 3.9 18.3 + - + +
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Residues in contact with ARG 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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56A ILE* 3.2 18.2 - - - +
57A PRO* 3.6 25.1 - - + +
58A GLU* 2.5 54.7 + - - +
95A SER* 2.9 29.8 + - - +
98A GLU* 1.3 76.3 - - + +
100A PHE* 1.3 66.1 + - - +
102A ILE* 3.0 23.5 + - + +
103A GLY 3.1 9.4 + - - -
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Residues in contact with PHE 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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57A PRO* 3.5 17.0 - - + +
60A VAL* 3.9 9.9 - - + -
61A GLY* 3.3 31.1 - - - -
64A ALA* 4.2 4.0 - - + -
84A ILE* 4.7 4.5 - - + -
86A LEU* 4.1 16.4 - - + -
96A TYR* 2.9 28.3 + + + +
97A VAL* 3.6 7.6 - - + +
99A ARG* 1.3 77.9 - - - +
101A TYR* 1.3 82.2 + + - +
102A ILE 3.1 0.5 + - - -
103A GLY 3.2 2.4 + - - -
104A VAL* 3.0 49.9 + - + +
128A ILE* 3.5 47.1 - - + -
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.7 29.6 - - + +
86A LEU* 3.4 20.4 - - + +
97A VAL* 3.0 33.6 + - + +
98A GLU* 3.7 1.6 - - - +
99A ARG 3.3 0.4 - - - -
100A PHE* 1.3 84.5 - + - +
102A ILE* 1.3 59.2 + - - +
104A VAL* 3.7 9.5 - - + +
105A LYS* 3.0 25.6 + - - +
307A ACP 2.8 30.5 + - - -
14B LEU* 5.6 0.4 - - + -
15B ILE* 3.5 44.0 - - + -
18B THR* 3.7 25.3 - - + +
19B LEU* 4.0 25.7 - - + +
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Residues in contact with ILE 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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58A GLU* 5.0 9.6 - - + +
98A GLU* 3.2 25.7 + - + +
99A ARG* 3.0 20.7 + - + +
101A TYR* 1.3 75.3 - - - +
103A GLY* 1.3 64.2 + - - +
104A VAL 3.1 1.3 - - - -
105A LYS* 3.2 11.0 + - + +
106A ARG* 2.8 44.4 + - - +
18B THR* 4.2 12.1 - - + -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.4 29.6 - - - +
62A TRP* 3.6 15.8 - - - +
99A ARG 3.1 10.1 + - - -
100A PHE 3.2 1.8 + - - -
102A ILE* 1.3 78.3 - - - +
104A VAL* 1.3 59.4 + - - +
106A ARG* 3.7 10.2 - - - +
107A ALA* 3.2 23.2 + - - +
187A ARG* 5.6 1.3 - - - -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 3.4 27.1 - - - +
64A ALA* 5.1 0.7 - - + -
65A ILE* 3.7 25.8 - - + -
84A ILE* 3.9 17.3 - - + -
100A PHE* 3.0 40.6 + - + +
101A TYR* 3.9 12.3 - - + +
103A GLY* 1.3 76.2 - - - +
105A LYS* 1.3 67.1 + - - +
107A ALA* 3.0 2.4 + - - +
108A CYS* 3.0 22.6 + - - -
115A VAL* 4.0 12.8 - - + -
19B LEU* 4.9 1.6 - - + -
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Residues in contact with LYS 105 (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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101A TYR 3.0 20.5 + - - +
102A ILE* 3.4 10.8 - - + +
104A VAL* 1.3 79.4 - - - +
106A ARG* 1.3 58.0 + - + +
108A CYS* 3.3 6.6 + - - +
109A GLU* 2.7 55.7 + - + +
18B THR* 3.3 27.4 - - + +
19B LEU* 4.1 24.8 + - + +
20B GLU* 3.4 31.1 + - - +
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Residues in contact with ARG 106 (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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58A GLU* 6.2 0.9 - - - -
62A TRP* 3.8 19.4 - - + -
102A ILE* 2.8 39.2 - - + +
103A GLY* 3.7 11.7 - - - +
105A LYS* 1.3 72.1 - - - +
107A ALA* 1.3 64.5 + - - +
108A CYS 3.2 1.6 - - - -
109A GLU* 3.7 18.3 - - + +
110A PHE* 3.1 22.9 + - - +
187A ARG* 5.6 9.9 - - - +
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Residues in contact with ALA 107 (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 TRP* 3.6 30.7 - - + +
65A ILE* 3.7 26.2 - - + -
103A GLY 3.2 18.8 + - - +
104A VAL 3.0 6.3 + - - +
106A ARG* 1.3 77.4 - - - +
108A CYS* 1.3 58.9 + - - +
110A PHE* 3.3 1.2 + - - +
111A TYR* 2.9 40.3 + - + -
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Residues in contact with CYS 108 (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 ILE* 4.0 14.6 - - - -
82A ALA* 5.3 0.4 - - - -
104A VAL 3.0 14.7 + - - +
105A LYS* 3.6 10.3 - - - +
107A ALA* 1.3 77.0 - - - +
109A GLU* 1.3 57.1 + - + +
112A LYS* 2.7 31.2 + - - -
113A CYS* 2.9 50.3 + - - +
114A GLU* 4.8 1.6 - - - -
115A VAL* 3.7 30.5 - - - +
19B LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 109 (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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105A LYS* 2.7 51.3 + - + +
106A ARG* 3.7 19.6 - - - +
107A ALA 3.3 0.2 - - - -
108A CYS* 1.3 78.1 - - - +
110A PHE* 1.3 62.1 + - - +
112A LYS* 3.6 15.0 + - - +
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Residues in contact with PHE 110 (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 TRP* 3.9 20.4 - + + -
106A ARG 3.1 18.6 + - - +
107A ALA 3.5 3.6 - - - +
109A GLU* 1.3 78.6 - - - +
111A TYR* 1.3 95.4 + + - +
112A LYS* 4.4 6.9 - - - +
189A THR* 4.2 19.5 - - + -
192A ILE* 4.6 15.5 - - + +
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Residues in contact with TYR 111 (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 TRP* 4.0 6.2 - + - -
65A ILE* 3.9 5.6 - - + -
66A SER* 2.6 39.0 + - - -
69A VAL* 3.8 30.3 - - + -
79A PRO* 4.4 8.4 - - + +
107A ALA* 2.9 33.7 + - + +
110A PHE* 1.3 104.0 - + - +
112A LYS* 1.3 71.3 - - - +
113A CYS* 4.4 9.2 - - - -
189A THR* 3.5 5.7 - - - +
190A ALA* 2.8 44.5 + - + -
192A ILE* 3.2 34.9 - - + +
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Residues in contact with LYS 112 (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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79A PRO 3.4 13.4 - - - +
80A LYS* 4.8 7.8 + - - +
108A CYS 2.7 12.8 + - - -
109A GLU* 4.0 13.0 - - - +
110A PHE 3.4 6.4 - - - +
111A TYR* 1.3 84.0 - - - +
113A CYS* 1.3 55.0 + - - +
192A ILE* 6.1 0.9 - - + -
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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
------------------------------------------------------------
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