Contacts of the helix formed by residues 99 - 112 (chain C) in PDB entry 4CEV
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 HIS 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ASP* 1.3 67.7 - - - +
100C SER* 1.3 59.7 + - - +
101C ILE 3.0 5.6 - - - -
102C ALA* 3.1 14.4 + - + -
120C TRP* 3.2 26.2 - + - -
122C ASP* 3.1 11.2 - - + -
126C ASP* 3.0 2.7 + - - -
139C HIS* 3.8 12.9 - - - +
142C PRO* 3.3 10.9 - - + +
224C SER* 2.7 28.8 + - - -
226C ASP* 3.4 18.8 + - + +
270C VAL* 3.5 22.6 - - + +
271C GLU* 2.9 16.8 + - - +
300C MN 2.1 39.4 + - - +
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C MET* 3.8 14.4 - - - +
14C GLY* 3.8 5.3 - - - -
71C VAL* 3.8 12.5 - - - +
75C ASN* 3.1 16.7 + - - +
98C ASP* 2.8 22.2 + - - -
99C HIS* 1.3 75.9 - - - +
101C ILE* 1.3 60.0 + - - +
102C ALA 3.1 2.4 + - - -
103C ILE* 3.3 14.0 + - - +
138C ILE* 4.0 17.9 - - - -
139C HIS* 3.8 23.0 - - - +
142C PRO* 4.2 7.2 - - - -
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Residues in contact with ILE 101 (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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9C VAL* 3.5 27.4 - - + +
11C MET* 3.7 25.4 - - + -
75C ASN* 3.3 8.3 - - - +
78C LEU* 3.2 14.2 - - + +
94C VAL* 3.7 26.0 - - + -
96C GLY* 3.7 22.7 - - - +
98C ASP 3.4 16.6 - - - +
99C HIS 3.0 1.0 - - - -
100C SER* 1.3 74.4 - - - +
102C ALA* 1.3 65.5 + - - +
103C ILE 3.0 2.9 - - - -
104C GLY 3.0 11.3 + - - -
105C THR* 3.1 11.3 + - - -
268C GLU* 4.0 3.6 - - - +
270C VAL* 3.7 25.8 - - + -
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Residues in contact with ALA 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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99C HIS* 3.1 20.4 + - + +
100C SER 3.1 0.6 - - - -
101C ILE* 1.3 80.2 - - - +
103C ILE* 1.3 63.6 + - - +
106C LEU* 2.9 32.8 + - + +
120C TRP* 3.6 29.6 - - + -
142C PRO* 3.9 3.6 - - + -
146C SER* 4.7 0.2 - - - -
268C GLU* 3.3 27.1 - - - +
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Residues in contact with ILE 103 (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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75C ASN* 3.9 8.1 - - + +
100C SER 3.4 15.3 - - - +
102C ALA* 1.3 77.8 - - - +
104C GLY* 1.3 62.3 + - - +
106C LEU* 4.3 1.2 - - - +
107C ALA* 3.2 24.5 + - - +
138C ILE* 4.2 14.4 - - + -
141C MET 4.8 0.2 - - - -
142C PRO* 3.5 33.8 - - + +
145C ALA* 4.1 15.5 - - + -
146C SER* 4.1 9.4 + - - +
154C LEU* 3.6 46.0 - - + +
157C ILE* 3.7 18.4 - - + -
163C LYS* 5.1 2.9 - - - +
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Residues in contact with GLY 104 (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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75C ASN* 2.8 46.2 + - - -
78C LEU* 3.8 11.2 - - - -
79C ALA* 3.3 12.3 - - - -
101C ILE 3.0 1.5 + - - -
103C ILE* 1.3 72.9 - - - +
105C THR* 1.3 64.1 + - - +
107C ALA* 3.2 4.5 + - - +
108C GLY 3.1 17.5 + - - -
157C ILE* 4.6 0.2 - - - -
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Residues in contact with THR 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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78C LEU* 3.4 13.5 - - - +
82C VAL* 3.8 10.9 - - + +
92C PRO* 5.8 1.3 - - + +
94C VAL* 3.8 25.8 - - + +
101C ILE 3.1 9.0 + - - -
102C ALA 3.8 4.0 - - - -
104C GLY* 1.3 74.0 - - - +
106C LEU* 1.3 63.2 + - - +
108C GLY 3.2 2.8 + - - -
109C VAL* 3.1 34.5 + - + +
222C HIS* 3.4 29.6 - - + +
266C SER* 5.4 1.3 - - - +
267C ALA 4.9 0.9 - - - +
268C GLU* 2.7 26.1 + - + +
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Residues in contact with LEU 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 ALA* 2.9 17.3 + - + +
103C ILE 4.3 0.9 - - - +
105C THR* 1.3 77.5 - - - +
107C ALA* 1.3 57.4 + - - +
109C VAL* 4.5 2.9 - - + -
110C ALA* 2.9 35.5 + - - +
116C LEU* 3.7 26.7 - - + -
118C VAL* 3.9 11.9 - - + -
120C TRP* 4.3 22.7 - - + -
146C SER* 3.5 32.5 - - - +
163C LYS* 3.9 9.9 - - + -
164C ILE* 4.2 13.9 - - + -
222C HIS* 3.6 31.0 - - + +
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Residues in contact with ALA 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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79C ALA* 3.7 16.8 - - + +
103C ILE 3.2 21.7 + - - +
104C GLY 3.4 5.8 - - - +
105C THR 3.2 0.4 - - - -
106C LEU* 1.3 76.6 - - - +
108C GLY* 1.3 56.0 + - - +
111C LYS* 3.7 7.1 + - - -
157C ILE* 3.7 17.7 - - + +
158C GLY* 4.6 0.8 - - - +
160C TYR* 2.4 33.7 + - - -
163C LYS* 3.7 22.4 - - - +
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Residues in contact with GLY 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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79C ALA* 3.5 25.1 - - - +
82C VAL* 4.1 5.2 - - - -
83C ASP* 3.5 12.9 - - - -
86C VAL* 4.2 1.6 - - - +
104C GLY 3.1 10.8 + - - -
105C THR 3.2 2.6 + - - -
107C ALA* 1.3 77.8 - - - +
109C VAL* 1.3 61.2 + - - +
111C LYS* 3.8 4.0 - - - +
112C HIS* 3.0 27.5 + - - -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C VAL* 3.5 19.1 - - + -
86C VAL* 4.4 5.8 - - + -
92C PRO* 4.2 5.6 - - + -
105C THR* 3.1 22.8 + - + +
106C LEU* 3.3 5.6 + - + +
108C GLY* 1.3 77.8 - - - +
110C ALA* 1.3 66.8 + - - +
111C LYS 3.3 2.2 - - - -
112C HIS* 2.9 19.6 + - - +
113C TYR* 3.3 27.8 - - + -
116C LEU* 3.9 16.8 - - + -
222C HIS* 5.0 0.4 - - - +
265C THR* 5.4 0.2 - - - +
266C SER* 3.7 34.5 - - - +
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Residues in contact with ALA 110 (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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106C LEU 2.9 22.9 + - - +
109C VAL* 1.3 74.1 - - - +
111C LYS* 1.3 53.2 + - - +
112C HIS 2.8 0.7 + - - -
113C TYR* 2.8 35.9 + - - +
116C LEU* 3.8 20.9 - - + +
160C TYR* 3.5 8.5 - - + +
163C LYS* 3.2 38.5 - - + +
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Residues in contact with LYS 111 (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 ALA* 6.1 1.4 - - - +
83C ASP* 3.6 26.2 + - - +
87C GLN* 5.6 0.4 - - - +
107C ALA 3.7 9.6 + - - +
108C GLY* 3.8 2.4 - - - +
110C ALA* 1.3 72.4 - - - +
112C HIS* 1.3 91.7 + - + +
113C TYR 3.4 2.6 + - - +
158C GLY* 4.0 14.3 + - - -
160C TYR* 2.9 51.7 + - + +
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Residues in contact with HIS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 2.6 33.6 + - - -
86C VAL* 3.5 28.9 - - + +
87C GLN* 3.7 23.1 - - + -
108C GLY 3.0 24.7 + - - -
109C VAL 2.9 10.1 + - - +
110C ALA 2.8 1.6 + - - -
111C LYS* 1.3 91.1 - - + +
113C TYR* 1.3 71.0 + - + +
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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