Contacts of the helix formed by residues 92 - 110 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C SER* 3.3 1.8 + - - -
90C GLY 3.9 0.4 + - - -
91C LYS* 1.3 79.8 - - - +
93C ILE* 1.3 64.6 + - - +
94C ASP* 3.5 7.5 + - - +
95C ASP* 3.0 31.2 + - - +
96C ALA 2.9 17.8 + - - -
310C GLY 5.9 0.9 - - - +
312C TYR* 4.7 9.2 - - - +
314C ASP 5.8 1.8 - - - +
315C GLU* 6.6 0.2 - - - -
317C ALA* 3.7 27.8 - - + +
318C ASP 4.1 16.2 - - - +
319C MSE 4.2 10.5 - - - +
320C GLY* 4.8 0.9 - - - +
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ASN 5.3 0.7 - - - +
82C ALA* 3.8 17.9 - - + +
83C GLU* 3.8 19.3 - - + +
86C SER* 3.5 19.6 + - - +
92C THR* 1.3 72.5 - - - +
94C ASP* 1.3 62.9 - - - +
96C ALA* 3.1 3.9 + - - +
97C LYS* 2.9 52.3 + - - +
312C TYR* 3.8 31.0 + - + +
315C GLU* 6.2 4.5 - - + -
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Residues in contact with ASP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 3.3 7.3 + - - +
93C ILE* 1.3 81.1 - - - +
95C ASP* 1.3 61.9 + - - +
97C LYS* 3.3 19.3 + - - +
98C GLY* 3.0 18.2 + - - -
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Residues in contact with ASP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LYS* 3.7 22.2 + - + +
92C THR* 3.0 39.7 + - - +
94C ASP* 1.3 75.8 - - - +
96C ALA* 1.3 58.1 + - - +
98C GLY* 3.1 4.1 + - - -
99C ASP* 2.9 28.2 + - - +
149C PHE* 5.7 0.7 - - - -
273C GLY* 5.2 1.7 - - - -
274C SER* 3.3 33.0 + - - -
318C ASP 4.8 2.8 - - - +
319C MSE 5.9 0.2 - - - -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 3.6 21.1 - - - +
85C LEU* 4.1 15.0 - - + +
86C SER* 3.4 24.0 - - - +
91C LYS* 4.1 6.0 - - - +
92C THR 2.9 5.6 + - - +
93C ILE 3.3 8.5 - - - +
95C ASP* 1.3 76.4 - - - +
97C LYS* 1.3 63.0 + - - +
99C ASP* 3.1 11.2 - - - +
100C ILE* 3.0 28.3 + - - +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C MSE 3.9 27.7 - - + +
79C ASN* 2.9 31.0 + - - +
82C ALA* 3.7 15.3 - - + -
93C ILE* 2.9 36.5 + - + +
94C ASP* 3.6 19.0 + - - +
95C ASP 3.3 0.2 - - - -
96C ALA* 1.3 74.3 - - - +
98C GLY* 1.3 52.4 + - - +
100C ILE* 3.4 2.4 + - - +
101C VAL* 2.8 42.2 + - + +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP 3.0 13.4 + - - -
95C ASP* 3.1 4.7 + - - -
97C LYS* 1.3 72.7 - - - +
99C ASP* 1.3 59.6 + - - +
101C VAL* 3.8 6.0 - - - +
102C ARG* 2.9 41.1 + - - +
149C PHE* 5.7 0.4 - - - -
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Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.6 9.7 - - - +
91C LYS* 2.8 30.8 + - - +
95C ASP 2.9 11.6 + - - +
96C ALA* 3.1 11.7 - - - +
98C GLY* 1.3 76.9 - - - +
100C ILE* 1.3 62.5 + - - +
102C ARG* 3.5 0.8 + - - +
103C GLY 3.3 5.7 + - - -
149C PHE* 3.2 35.7 - - + -
150C PRO* 3.4 7.4 - - - +
151C GLY* 3.2 5.9 + - - -
152C MSE 2.6 51.5 + - - +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 4.6 11.4 - - + -
78C MSE 3.8 31.6 - - + -
81C LEU* 3.6 32.3 - - + +
82C ALA* 3.5 32.5 - - - +
85C LEU* 4.3 11.7 - - + -
96C ALA 3.0 17.9 + - - +
97C LYS* 3.7 4.3 - - - +
99C ASP* 1.3 74.3 - - - +
101C VAL* 1.3 59.4 + - - +
103C GLY* 3.1 3.3 + - - -
104C LEU* 2.8 25.5 + - + +
151C GLY* 5.4 2.5 - - - -
155C MSE 3.7 18.5 - - + +
179C VAL* 5.5 3.8 - - + -
183C LEU* 5.7 0.4 - - + -
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 5.4 1.8 - - - +
75C ASN* 5.6 0.9 - - - +
78C MSE 3.7 21.3 - - + -
97C LYS* 2.8 28.0 + - + +
98C GLY* 3.3 7.2 + - - +
100C ILE* 1.3 73.2 - - - +
102C ARG* 1.3 58.8 + - + +
104C LEU* 3.1 15.5 + - + +
105C GLU* 2.8 48.1 + - + +
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLY* 2.9 22.1 + - - +
99C ASP 4.0 0.2 - - - +
101C VAL* 1.3 75.8 - - + +
103C GLY* 1.3 63.4 + - - +
105C GLU* 3.5 21.5 + - - +
106C VAL* 3.5 18.9 + - - +
149C PHE* 3.6 23.8 - - - -
152C MSE 3.3 42.0 - - + +
156C TRP* 4.7 8.3 + - - +
278C ARG* 2.9 33.2 - - - +
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Residues in contact with GLY 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASP 3.3 7.3 + - - -
100C ILE 3.1 6.7 + - - -
102C ARG* 1.3 73.0 - - - +
104C LEU* 1.3 65.9 + - - +
105C GLU 3.1 0.2 - - - -
106C VAL* 3.1 16.9 + - - +
107C CYS* 3.3 14.4 + - - -
152C MSE 3.9 12.2 - - - +
155C MSE 3.5 33.8 - - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 4.7 3.8 - - - +
71C VAL* 4.1 12.5 - - + +
74C LEU* 3.8 37.9 - - + -
75C ASN* 3.7 32.8 - - - +
78C MSE 4.3 11.0 - - + -
100C ILE 2.8 12.6 + - - +
101C VAL* 3.2 20.0 - - + +
103C GLY* 1.3 73.7 - - - +
105C GLU* 1.3 61.1 + - + +
107C CYS* 3.2 8.1 + - - +
108C GLU* 3.0 52.6 + - + +
155C MSE 3.8 1.6 - - - -
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Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.5 31.7 + - - +
65A ARG* 3.0 32.0 + - - +
101C VAL* 2.8 34.0 + - + +
102C ARG* 3.9 18.5 - - - +
103C GLY 3.1 0.8 - - - -
104C LEU* 1.3 79.5 - - + +
106C VAL* 1.3 61.1 + - + +
108C GLU* 3.4 10.5 + - - +
109C PHE* 3.2 21.1 + - - +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ARG 3.5 16.2 - - - +
103C GLY* 3.1 7.7 + - - +
105C GLU* 1.3 75.2 - - - +
107C CYS* 1.3 63.6 + - - +
109C PHE* 3.2 13.2 + - + +
110C VAL* 3.1 25.0 + - + +
155C MSE 3.9 18.8 - - - +
156C TRP* 3.6 39.0 - - + +
159C ALA* 4.0 0.9 - - + -
160C PRO* 3.9 14.1 - - + -
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Residues in contact with CYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.9 15.2 - - + +
70C PHE* 3.7 31.9 - - + -
71C VAL* 3.7 17.9 - - + -
103C GLY 3.6 12.6 - - - -
104C LEU* 3.2 10.2 + - - +
106C VAL* 1.3 76.4 - - - +
108C GLU* 1.3 61.3 + - - +
110C VAL* 3.5 12.4 - - - +
111C ILE* 3.4 24.3 + - - +
155C MSE 4.0 11.9 - - - -
158C PHE* 5.0 1.3 - - - -
159C ALA* 4.2 14.4 - - - -
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 4.6 8.8 + - - +
65A ARG* 2.8 45.2 + - - +
68A MSE 3.5 30.2 - - + +
111A ILE* 4.3 10.5 - - + +
112A GLY* 5.7 1.0 - - - -
71C VAL* 4.1 11.8 - - + +
104C LEU* 3.0 34.8 + - + +
105C GLU* 3.4 14.6 - - - +
106C VAL 3.2 0.2 - - - -
107C CYS* 1.3 76.6 - - - +
109C PHE* 1.3 62.3 + - - +
111C ILE* 3.3 26.6 - - - +
112C GLY 4.3 0.7 + - - -
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLY* 5.7 4.3 - - - -
114A PRO* 6.5 0.4 - - + -
115A HIS* 4.1 31.6 - + + -
118A LYS* 5.1 4.5 - - - -
105C GLU 3.2 10.3 + - - +
106C VAL* 3.5 15.5 - - + +
108C GLU* 1.3 79.5 - - - +
110C VAL* 1.3 70.8 + - + +
111C ILE 3.2 0.2 - - - -
112C GLY* 3.0 17.0 + - - -
116C LEU* 3.6 42.2 - - + +
160C PRO* 6.2 2.0 - - + -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.4 2.9 - - - +
67C PHE* 3.8 23.0 - - + -
106C VAL* 3.1 14.4 + - + +
107C CYS 3.5 13.0 - - - +
109C PHE* 1.3 87.9 - - + +
111C ILE* 1.3 64.3 + - - +
112C GLY 3.0 1.1 - - - -
113C ILE* 3.1 27.1 + - + +
116C LEU* 4.6 4.9 - - + -
159C ALA* 3.7 17.5 - - + +
160C PRO* 3.7 34.8 - - + -
163C ALA* 3.6 13.4 - - + +
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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