Contacts of the helix formed by residues 92 - 111 (chain A) in PDB entry 4IYM
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A SER* 3.1 5.7 + - - -
90A GLY 4.0 0.2 + - - -
91A LYS* 1.3 76.7 - - - +
93A ILE* 1.3 65.5 + - - +
94A ASP* 3.4 8.3 + - - +
95A ASP* 3.0 35.0 + - - +
96A ALA 2.9 18.7 + - - -
310A GLY 5.9 0.7 - - - +
312A TYR* 4.6 9.2 - - - +
314A ASP 5.8 2.0 - - - +
315A GLU* 6.4 2.2 - - - -
317A ALA* 3.6 27.4 - - + +
318A ASP 4.0 16.6 - - - +
319A MSE 4.2 9.6 - - - +
320A GLY* 4.8 0.9 - - - +
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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
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79A ASN 5.7 0.9 - - - +
82A ALA* 4.0 6.5 - - + +
83A GLU* 3.9 22.4 - - + +
86A SER* 3.5 17.0 + - - +
92A THR* 1.3 72.3 - - - +
94A ASP* 1.3 62.0 + - - +
96A ALA* 3.1 5.4 + - - +
97A LYS* 2.9 55.8 + - + +
312A TYR* 3.8 36.5 + - + +
315A GLU* 3.5 29.5 - - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.3 7.0 + - - +
93A ILE* 1.3 80.5 - - - +
95A ASP* 1.3 63.1 + - - +
97A LYS* 3.2 17.4 + - - +
98A GLY* 3.0 19.9 + - - -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.5 27.1 + - + +
92A THR* 3.0 41.9 + - - +
94A ASP* 1.3 74.1 - - - +
96A ALA* 1.3 64.0 + - - +
98A GLY* 3.1 4.3 + - - -
99A ASP* 3.0 21.3 + - - +
149A PHE* 5.6 1.6 - - - -
273A GLY* 5.7 1.6 - - - -
274A SER* 3.8 26.5 + - - +
318A ASP 4.8 3.3 - - - +
319A MSE 5.7 0.9 - - - -
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Residues in contact with ALA 96 (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 ALA* 3.6 23.3 - - + +
85A LEU* 3.9 15.1 - - + +
86A SER* 3.3 25.4 - - - +
91A LYS* 4.1 6.7 - - + +
92A THR 2.9 5.6 + - - +
93A ILE 3.1 6.7 + - - +
95A ASP* 1.3 75.5 - - - +
97A LYS* 1.3 57.1 + - - +
99A ASP* 3.0 26.1 - - - +
100A ILE* 3.1 15.8 + - - +
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Residues in contact with LYS 97 (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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78A MSE 3.9 27.0 - - + +
79A ASN* 2.9 30.2 + - - +
82A ALA* 3.8 15.5 - - + -
93A ILE* 2.9 36.5 + - + +
94A ASP* 3.6 17.8 + - - +
96A ALA* 1.3 72.7 - - - +
98A GLY* 1.3 54.7 - - - +
100A ILE* 3.2 2.3 + - - +
101A VAL* 2.8 43.2 + - + +
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Residues in contact with GLY 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 ASP 3.0 14.2 + - - -
95A ASP* 3.1 5.1 + - - -
97A LYS* 1.3 73.0 - - - +
99A ASP* 1.3 62.8 + - - +
101A VAL* 3.9 6.2 - - - +
102A ARG* 3.0 36.1 + - - +
149A PHE* 5.8 0.9 - - - -
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Residues in contact with ASP 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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85A LEU* 3.7 12.1 - - + +
91A LYS* 2.8 28.4 + - - +
95A ASP 3.0 11.2 + - - +
96A ALA 3.0 13.5 - - - +
98A GLY* 1.3 75.6 - - - +
100A ILE* 1.3 61.8 + - - +
102A ARG* 5.1 0.4 - - - -
103A GLY 3.3 6.9 + - - -
149A PHE* 3.2 33.6 - - + -
150A PRO* 3.4 6.6 - - - +
151A GLY* 3.2 6.0 + - - -
152A MSE 2.7 53.4 + - - +
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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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74A LEU* 4.6 14.4 - - + -
78A MSE 3.5 32.3 - - + -
81A LEU* 4.2 36.3 - - + -
82A ALA 4.8 2.9 - - - +
85A LEU* 3.9 21.1 - - + -
96A ALA 3.1 13.6 + - - +
97A LYS* 3.2 6.7 + - - +
99A ASP* 1.3 77.9 - - - +
101A VAL* 1.3 57.5 + - - +
103A GLY* 3.1 4.0 + - - -
104A LEU* 2.8 26.4 + - + +
151A GLY* 4.2 9.0 - - - -
155A MSE 3.6 10.5 - - + +
179A VAL* 4.1 19.7 - - + -
183A LEU* 5.1 0.4 - - + -
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Residues in contact with VAL 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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75A ASN* 5.7 0.2 - - - +
78A MSE 3.8 21.8 - - + -
97A LYS* 2.8 27.1 + - + +
98A GLY* 3.9 7.2 - - - +
100A ILE* 1.3 73.2 - - - +
102A ARG* 1.3 61.3 + - + +
104A LEU* 3.1 16.2 + - + +
105A GLU* 3.0 47.0 + - + +
65C ARG* 5.3 2.0 - - - +
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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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98A GLY* 3.0 22.0 + - - +
99A ASP 4.1 0.2 - - - +
100A ILE 3.3 0.4 - - - -
101A VAL* 1.3 77.2 - - + +
103A GLY* 1.3 64.3 + - - +
105A GLU* 3.5 22.4 + - - +
106A VAL* 3.7 15.6 + - - +
149A PHE* 4.5 6.6 - - - -
152A MSE 3.3 46.2 - - + +
156A TRP* 4.7 2.1 + - - +
278A ARG* 3.2 36.4 - - - +
439A ILE* 5.5 1.0 - - - +
441A VAL* 3.7 32.7 - - - +
443A LEU* 6.1 4.5 - - - -
444A ALA* 5.1 0.9 - - - +
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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
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99A ASP 3.3 7.3 + - - -
100A ILE 3.1 6.8 + - - -
102A ARG* 1.3 75.2 - - - +
104A LEU* 1.3 64.2 + - - +
106A VAL* 3.0 18.0 + - - +
107A CYS* 3.3 13.0 + - - -
152A MSE 3.8 16.9 - - - +
155A MSE 3.6 28.7 - - - +
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Residues in contact with LEU 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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71A VAL* 3.9 13.2 - - + +
74A LEU* 3.8 39.5 - - + -
75A ASN* 3.5 32.1 - - - +
78A MSE 4.4 11.0 - - + -
100A ILE 2.8 13.2 + - - +
101A VAL* 3.2 17.9 - - + +
103A GLY* 1.3 74.5 - - - +
105A GLU* 1.3 60.4 + - + +
107A CYS* 3.1 8.2 + - - +
108A GLU* 2.9 55.7 + - + +
155A MSE 3.9 1.2 - - - -
65C ARG* 4.6 4.7 - - - +
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Residues in contact with GLU 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 VAL* 3.0 33.3 + - + +
102A ARG* 3.8 16.4 - - - +
103A GLY 3.1 0.4 - - - -
104A LEU* 1.3 77.2 - - + +
106A VAL* 1.3 59.6 + - - +
108A GLU* 3.5 11.0 + - - +
109A PHE* 3.1 20.3 + - - +
443A LEU* 3.9 16.6 - - - +
444A ALA* 3.2 17.4 + - + +
61C GLN* 3.2 30.5 + - - +
65C ARG* 3.1 30.2 + - - +
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Residues in contact with VAL 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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102A ARG 3.7 9.6 + - - +
103A GLY 3.0 7.9 + - - +
105A GLU* 1.3 73.9 - - - +
107A CYS* 1.3 61.5 + - - +
109A PHE* 3.1 6.6 + - + +
110A VAL* 3.0 30.7 + - + +
155A MSE 3.9 10.3 - - - +
156A TRP* 3.7 34.8 - - + +
159A ALA* 3.8 17.5 - - + -
160A PRO* 4.0 12.3 - - + -
444A ALA* 3.7 16.4 - - + -
462A HIS* 4.1 21.1 - - + -
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Residues in contact with CYS 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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67A PHE* 3.8 14.2 - - + +
70A PHE* 3.8 32.1 - - + -
71A VAL* 3.7 18.2 - - + -
103A GLY 3.3 12.5 + - - -
104A LEU* 3.1 12.7 + - - +
106A VAL* 1.3 72.7 - - - +
108A GLU* 1.3 61.9 + - - +
110A VAL* 3.3 23.5 - - - +
111A ILE* 3.3 13.7 + - - +
155A MSE 4.0 11.9 - - - -
158A PHE* 5.2 1.3 - - - -
159A ALA* 4.1 14.6 - - - -
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Residues in contact with GLU 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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71A VAL* 4.0 15.6 - - + +
104A LEU* 2.9 30.6 + - - +
105A GLU* 3.6 15.6 - - - +
106A VAL 3.3 0.2 - - - -
107A CYS* 1.3 75.5 - - - +
109A PHE* 1.3 64.0 + - - +
111A ILE* 3.3 27.4 + - - +
112A GLY 4.3 0.5 + - - -
61C GLN* 4.5 7.5 + - - +
65C ARG* 2.7 44.8 + - - +
68C MSE 3.4 32.7 - - + +
111C ILE* 4.4 9.0 - - + +
112C GLY* 5.8 1.7 - - - -
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Residues in contact with PHE 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 GLU 3.1 14.7 + - - +
106A VAL* 3.1 15.7 + - + +
108A GLU* 1.3 77.6 - - - +
110A VAL* 1.3 68.7 + - + +
112A GLY* 3.1 16.8 + - - -
116A LEU* 3.6 45.5 - - + +
444A ALA* 3.8 16.2 - - + -
445A TYR* 3.7 32.1 - - + +
462A HIS* 5.1 0.4 - - + -
463A GLY* 3.4 42.8 - - - -
464A THR* 4.1 1.8 - - + -
466A SER* 4.5 1.8 - - - -
467A ILE* 4.5 7.4 - - + -
112C GLY* 5.7 3.1 - - - -
115C HIS* 4.1 15.5 - + + -
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Residues in contact with VAL 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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64A ALA* 4.4 1.9 - - - +
67A PHE* 3.6 32.5 - - + -
106A VAL* 3.0 19.8 + - + +
107A CYS* 3.3 15.7 - - - +
109A PHE* 1.3 87.1 - - + +
111A ILE* 1.3 65.8 + - - +
112A GLY 2.9 1.1 - - - -
113A ILE* 2.9 26.4 + - + +
116A LEU* 4.6 3.1 - - - -
159A ALA* 3.8 8.1 - - + +
160A PRO* 3.7 35.0 - - + -
163A ALA* 3.6 11.8 - - + +
467A ILE* 5.0 4.9 - - + -
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Residues in contact with ILE 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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64A ALA* 3.2 24.8 - - + +
67A PHE* 4.2 3.8 - - + +
68A MSE 3.7 65.1 - - + +
71A VAL* 4.8 1.8 - - + -
107A CYS 3.3 13.9 + - - +
108A GLU* 3.3 26.2 - - - +
109A PHE 3.2 0.2 - - - -
110A VAL* 1.3 76.2 - - - +
112A GLY* 1.3 54.3 + - - +
113A ILE 3.2 2.1 + - - -
114A PRO* 3.4 5.7 - - - +
68C MSE 4.2 16.2 - - - -
108C GLU* 4.3 10.3 - - + +
111C ILE* 4.2 24.0 - - + -
112C GLY 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
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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