Contacts of the helix formed by residues 99 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP* 1.3 67.2 - - - +
100A SER* 1.3 60.6 + - - +
101A ILE 3.0 6.9 + - - -
102A ALA* 3.0 22.2 + - + +
120A TRP* 3.2 27.1 - + - -
122A ASP* 3.0 17.5 - - - -
126A ASP* 2.9 3.1 + - - -
139A HIS* 3.7 15.2 - - - +
142A PRO* 3.5 6.8 - - + +
224A SER* 2.8 31.6 + - - -
226A ASP* 3.5 16.4 + - + +
270A VAL* 3.7 21.4 - - + +
271A GLU* 2.8 16.0 + - + +
300A MN 2.1 31.6 + - - +
401A ORN 4.7 0.2 - - - +
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Residues in contact with SER 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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11A MET* 3.8 11.6 - - - +
14A GLY* 3.8 7.8 - - - -
71A VAL* 3.8 12.0 - - - +
75A ASN* 3.1 17.1 + - - +
98A ASP* 2.8 21.9 + - - -
99A HIS* 1.3 76.4 - - - +
101A ILE* 1.3 61.1 + - - +
102A ALA 3.1 0.2 - - - -
103A ILE* 3.3 14.1 + - - +
138A ILE* 3.8 27.8 - - - -
139A HIS* 3.7 14.9 - - - +
142A PRO* 4.3 7.4 - - - -
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Residues in contact with ILE 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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9A VAL* 3.4 27.8 - - + +
11A MET* 3.6 26.0 - - + -
75A ASN* 3.3 7.9 - - - +
78A LEU* 3.1 12.7 - - + +
94A VAL* 3.7 27.6 - - + -
96A GLY* 3.7 28.9 - - - +
98A ASP 3.4 16.8 - - - +
99A HIS 3.0 1.4 - - - -
100A SER* 1.3 74.0 - - - +
102A ALA* 1.3 67.2 + - - +
103A ILE 2.9 2.7 - - - -
104A GLY 3.0 11.8 + - - -
105A THR* 3.1 10.4 + - - -
268A GLU* 3.9 7.4 - - + +
270A VAL* 3.8 15.5 - - + -
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Residues in contact with ALA 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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99A HIS* 3.0 20.6 + - + +
101A ILE* 1.3 81.6 - - - +
103A ILE* 1.3 63.7 + - - +
106A LEU* 3.0 31.1 + - + +
120A TRP* 3.5 30.3 - - + -
142A PRO* 3.9 2.5 - - + -
146A SER* 4.7 1.6 - - - -
268A GLU* 3.3 28.5 - - - +
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Residues in contact with ILE 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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75A ASN* 3.9 8.7 - - - +
100A SER 3.4 15.7 - - - +
101A ILE 2.9 0.4 - - - -
102A ALA* 1.3 78.7 - - - +
104A GLY* 1.3 60.7 + - - +
106A LEU* 4.1 1.2 - - - +
107A ALA* 3.2 23.9 + - - +
138A ILE* 4.2 13.9 - - + -
141A MET 4.9 0.2 - - - -
142A PRO* 3.5 34.1 - - + +
145A ALA* 4.1 14.6 - - + -
146A SER* 4.1 10.0 + - - +
154A LEU* 3.5 47.8 - - + +
157A ILE* 3.7 17.9 - - + -
163A LYS* 5.1 2.8 - - - +
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Residues in contact with GLY 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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75A ASN* 2.8 46.1 + - - -
78A LEU* 3.6 9.6 - - - -
79A ALA* 3.2 12.6 - - - +
101A ILE 3.0 1.1 + - - -
103A ILE* 1.3 71.5 - - - +
105A THR* 1.3 65.3 + - - +
107A ALA* 3.2 3.8 + - - -
108A GLY 3.2 16.8 + - - -
157A ILE* 4.6 0.4 - - - -
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Residues in contact with THR 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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78A LEU* 3.2 13.0 - - - +
82A VAL* 3.7 9.9 - - + +
92A PRO* 5.7 1.1 - - + -
94A VAL* 3.6 28.3 - - + +
101A ILE 3.1 8.1 + - - -
102A ALA 3.9 3.1 - - - -
104A GLY* 1.3 75.9 - - - +
106A LEU* 1.3 62.2 + - - +
108A GLY 3.2 10.4 + - - -
109A VAL* 3.2 26.7 + - + +
222A HIS* 3.4 28.9 - - + +
266A SER* 5.4 1.6 - - - +
267A ALA 5.0 1.3 - - - +
268A GLU* 2.8 26.8 + - + +
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Residues in contact with LEU 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 ALA* 3.0 18.0 + - + +
103A ILE 4.4 0.4 - - - +
105A THR* 1.3 77.3 - - - +
107A ALA* 1.3 58.1 + - - +
109A VAL* 4.5 3.1 - - + +
110A ALA* 3.0 35.7 + - - +
116A LEU* 3.9 13.0 - - + -
118A VAL* 3.9 15.7 - - + -
120A TRP* 4.3 22.9 - - + -
146A SER* 3.4 32.8 - - - +
163A LYS* 3.5 10.4 - - + +
164A ILE* 4.2 14.4 - - + -
222A HIS* 3.3 39.7 - - + +
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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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79A ALA* 3.7 16.3 - - + +
103A ILE 3.2 21.1 + - - +
104A GLY 3.5 6.1 - - - +
105A THR 3.2 0.6 - - - -
106A LEU* 1.3 76.1 - - - +
108A GLY* 1.3 57.8 + - - +
111A LYS* 3.8 5.4 + - - +
157A ILE* 3.7 16.8 - - + +
158A GLY* 4.6 1.6 - - - +
160A TYR* 2.5 31.7 + - - -
163A LYS* 3.7 22.4 - - - +
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Residues in contact with GLY 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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79A ALA* 3.5 24.7 - - - +
82A VAL* 3.9 8.6 - - - +
83A ASP* 3.5 11.0 - - - -
86A VAL* 4.3 0.5 - - - +
104A GLY 3.2 9.8 + - - -
105A THR 3.2 2.6 + - - -
107A ALA* 1.3 79.0 - - - +
109A VAL* 1.3 59.3 + - - +
111A LYS* 3.7 4.8 - - - +
112A HIS* 3.0 26.7 + - - -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.5 18.4 - - + -
86A VAL* 4.3 5.6 - - + -
92A PRO* 4.1 6.1 - - + -
105A THR* 3.2 21.4 + - + +
106A LEU* 4.2 4.3 - - + +
108A GLY* 1.3 77.4 - - - +
110A ALA* 1.3 67.6 + - - +
111A LYS 3.3 1.8 - - - -
112A HIS* 2.9 25.7 + - - +
113A TYR* 3.3 24.7 - - + +
116A LEU* 3.8 17.0 - - + -
222A HIS* 5.2 0.4 - - - +
265A THR 5.8 0.2 - - - +
266A SER* 3.8 33.7 - - - +
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Residues in contact with ALA 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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106A LEU 3.0 19.6 + - - +
109A VAL* 1.3 77.2 - - - +
111A LYS* 1.3 58.7 + - - +
112A HIS 2.8 6.8 + - - -
113A TYR* 2.8 22.9 + - - +
116A LEU* 3.7 22.4 - - + +
160A TYR* 3.5 6.7 - - + +
163A LYS* 3.2 36.3 - - + +
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Residues in contact with LYS 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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83A ASP* 3.1 31.3 + - - +
87A GLN* 5.4 1.6 - - - +
107A ALA 3.8 7.4 + - - +
108A GLY* 3.7 11.6 - - - +
110A ALA* 1.3 69.3 - - - +
112A HIS* 1.3 89.3 + - + +
113A TYR 3.6 2.6 + - - +
158A GLY* 5.0 7.9 + - - -
160A TYR* 2.9 42.9 + - + +
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 2.7 34.9 + - - -
86A VAL* 3.5 30.0 - - + +
87A GLN* 3.7 22.6 - - + -
108A GLY 3.0 24.3 + - - -
109A VAL 2.9 11.4 + - - +
110A ALA 2.8 0.8 + - - -
111A LYS* 1.3 89.1 - - + +
113A TYR* 1.3 71.1 + - + -
219A ASP* 4.9 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