Contacts of the helix formed by residues 89 - 108 (chain A) in PDB entry 6EBT
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 PRO 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG 3.2 6.5 - - - +
88A MET* 1.3 98.8 - - + +
90A THR* 1.3 66.2 + - - +
91A PRO* 3.9 6.7 - - + -
92A VAL* 2.9 22.6 + - + +
93A ILE* 3.4 4.2 + - - +
140A VAL* 4.1 10.1 - - + -
413A ILE* 5.6 0.4 - - + -
414A LYS* 3.8 39.3 - - + +
417A LEU* 3.8 29.2 - - + -
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 5.3 5.4 + - - -
88A MET 3.3 4.8 + - - -
89A PRO* 1.3 70.3 - - - +
91A PRO* 1.3 71.4 - - + +
93A ILE* 2.9 12.5 + - + +
94A LYS* 2.9 50.4 + - + +
133A ASN* 3.7 31.4 + - - +
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.3 10.3 - - + -
90A THR* 1.3 96.0 - - + +
92A VAL* 1.3 55.8 + - - +
94A LYS* 3.6 10.7 + - + +
95A ALA* 3.0 28.8 + - - +
198A ALA* 3.5 14.1 - - + +
202A GLU* 3.8 29.6 - - - +
417A LEU* 4.0 20.2 - - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.1 20.4 - - + -
89A PRO* 2.9 16.3 + - + +
91A PRO* 1.3 73.0 - - - +
93A ILE* 1.3 66.9 + - - +
95A ALA* 3.1 4.3 + - - +
96A PHE* 2.9 45.5 + - + -
149A THR* 4.8 0.9 - - + -
191A PHE* 4.2 12.6 - - + -
194A ALA* 4.3 8.5 - - + +
195A MET* 5.2 0.9 - - - -
198A ALA* 4.1 7.9 - - + -
413A ILE* 3.9 24.5 - - + -
417A LEU* 3.7 24.0 - - + -
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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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88A MET* 4.2 19.1 - - + +
89A PRO 3.9 10.5 - - - +
90A THR* 2.9 14.7 + - + +
92A VAL* 1.3 76.1 - - - +
94A LYS* 1.3 63.1 + - - +
96A PHE* 3.0 17.2 + - - +
97A GLY 3.0 9.5 + - - -
127A VAL* 3.4 14.8 - - + +
133A ASN* 4.9 9.0 - - - +
136A PHE* 3.5 66.9 - - + -
149A THR* 3.8 26.7 - - + -
153A VAL* 4.7 1.6 - - + -
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 2.9 39.6 + - + +
91A PRO* 3.9 7.4 - - + +
93A ILE* 1.3 75.4 - - - +
95A ALA* 1.3 62.7 + - - +
97A GLY* 3.0 11.4 + - - -
98A ILE* 3.1 17.5 + - + +
127A VAL 3.6 15.5 - - - +
128A ALA* 3.4 25.9 - - - +
129A GLU 4.5 2.8 + - - -
130A GLY* 3.6 26.2 - - - +
133A ASN* 4.6 4.0 - - - +
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Residues in contact with ALA 95 (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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91A PRO 3.0 19.8 + - - +
92A VAL 3.5 4.0 - - - +
94A LYS* 1.3 76.7 - - - +
96A PHE* 1.3 59.1 + - - +
98A ILE* 3.3 7.4 + - - +
99A LEU* 2.9 28.3 + - - +
194A ALA* 3.3 30.1 - - - +
197A ILE* 3.7 28.6 - - + +
198A ALA* 3.8 4.3 - - - +
201A ILE* 5.8 1.1 - - + -
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Residues in contact with PHE 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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92A VAL* 2.9 33.9 + - + -
93A ILE* 3.0 8.9 + - - +
95A ALA* 1.3 74.5 - - - +
97A GLY* 1.3 55.4 + - - +
99A LEU* 3.0 8.2 + - + -
100A LYS* 2.7 59.5 + - - +
149A THR* 3.9 9.6 - - + -
150A ASN* 3.5 32.1 - - + -
153A VAL* 3.6 27.6 - - + -
190A THR* 4.0 17.0 - - - -
191A PHE* 3.7 41.5 - + + -
194A ALA* 3.4 16.2 - - + -
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Residues in contact with GLY 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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93A ILE 3.0 7.9 + - - -
94A LYS 3.0 8.2 + - - -
96A PHE* 1.3 76.2 - - - +
98A ILE* 1.3 63.1 + - - +
100A LYS* 4.8 1.3 - - - -
101A ARG* 2.9 25.1 + - - +
124A ALA* 3.4 29.3 - - - +
127A VAL* 4.0 9.3 - - - +
128A ALA* 4.0 9.0 - - - -
157A ILE* 5.0 1.8 - - - -
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Residues in contact with ILE 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 LYS* 3.1 16.1 + - + +
95A ALA* 3.6 7.2 - - - +
97A GLY* 1.3 74.2 - - - +
99A LEU* 1.3 64.8 + - - +
101A ARG* 3.2 8.2 + - - +
102A ALA* 3.0 21.0 + - - +
128A ALA* 3.8 15.0 - - + +
197A ILE* 4.1 9.9 - - + -
201A ILE* 3.8 28.7 - - + -
297A VAL* 4.2 16.2 - - + -
300A LEU* 4.0 19.0 - - + +
301A THR* 3.9 26.0 - - + -
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Residues in contact with LEU 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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95A ALA 2.9 17.3 + - - +
96A PHE* 3.0 15.0 + - + +
98A ILE* 1.3 79.1 - - - +
100A LYS* 1.3 62.7 - - + +
102A ALA* 3.1 5.5 + - - +
103A ALA* 2.9 29.3 + - + +
185A GLN* 5.0 2.9 - - + +
190A THR* 3.3 50.0 - - + +
193A THR* 3.8 24.5 - - + -
194A ALA* 4.3 3.6 - - + +
197A ILE* 4.4 6.3 - - + -
274A ALA* 4.6 5.2 - - + -
293A VAL* 4.2 20.9 - - + -
297A VAL* 4.7 5.6 - - + -
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Residues in contact with LYS 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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96A PHE* 2.7 33.1 + - + +
97A GLY 4.1 1.3 - - - +
99A LEU* 1.3 71.7 - - + +
101A ARG* 1.3 65.5 + - - +
103A ALA* 4.0 3.7 - - - +
104A ALA* 3.0 27.0 + - - +
120A ILE* 4.4 3.9 - - + +
124A ALA* 4.2 3.8 - - + -
150A ASN* 2.9 27.2 + - - -
153A VAL* 3.7 13.2 - - + -
154A ASN* 3.0 23.0 + - - +
157A ILE* 3.6 30.5 - - + -
181A VAL* 3.8 17.2 + - + +
182A ASN* 3.1 9.5 + - - -
185A GLN* 2.6 29.7 + - - +
190A THR* 4.5 2.6 - - - +
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Residues in contact with ARG 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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97A GLY 2.9 14.5 + - - +
98A ILE* 3.3 10.8 - - - +
100A LYS* 1.3 76.7 - - - +
102A ALA* 1.3 63.2 + - - +
104A ALA* 3.9 1.7 - - - +
105A GLU* 2.2 60.3 + - - +
121A MET* 3.5 42.0 - - - +
124A ALA* 3.6 11.5 - - + +
125A ASP* 3.2 32.6 + - - +
300A LEU* 3.7 34.6 - - + +
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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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98A ILE 3.0 10.1 + - - +
99A LEU 3.1 7.4 + - - +
101A ARG* 1.3 77.5 - - - +
103A ALA* 1.3 62.5 + - - +
105A GLU* 3.4 3.1 + - - +
106A VAL* 3.1 28.9 + - - +
293A VAL* 4.0 7.4 - - + +
296A LYS* 3.5 31.1 - - + +
297A VAL* 3.7 28.3 - - + +
300A LEU* 4.1 3.4 - - + -
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Residues in contact with ALA 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 LEU* 2.9 20.3 + - + +
100A LYS* 4.0 4.3 - - - +
102A ALA* 1.3 73.9 - - - +
104A ALA* 1.3 66.8 + - - +
106A VAL* 2.9 3.2 + - - +
107A THR* 2.8 29.3 + - - +
183A LYS 5.1 0.9 - - - +
185A GLN* 3.5 36.1 - - + +
289A PHE* 4.7 11.2 - - + -
293A VAL* 4.5 12.9 - - + +
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Residues in contact with ALA 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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100A LYS 3.0 18.8 + - - +
101A ARG 3.9 3.1 - - - +
103A ALA* 1.3 76.0 - - - +
105A GLU* 1.3 62.2 + - - +
107A THR* 3.3 9.8 + - - -
108A GLN* 3.3 25.8 + - - +
112A LEU* 4.0 10.7 - - + +
117A ALA* 4.0 4.0 - - - +
120A ILE* 3.6 28.3 - - + -
121A MET* 4.0 13.9 - - + -
180A HIS 5.8 2.7 - - - +
181A VAL 6.0 0.2 + - - -
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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 ARG* 2.2 52.0 + - - +
102A ALA* 3.7 5.8 - - - +
103A ALA 3.1 0.8 - - - -
104A ALA* 1.3 76.7 - - - +
106A VAL* 1.3 60.8 + - + +
108A GLN* 3.5 31.4 + - - +
109A ASP* 4.5 5.0 + - - +
121A MET* 4.2 14.3 - - + -
296A LYS* 4.0 18.6 - - + +
300A LEU* 5.2 0.2 - - - +
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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 ALA 3.1 17.0 + - - +
103A ALA 2.9 5.1 + - - +
105A GLU* 1.3 77.0 - - + +
107A THR* 1.3 59.9 + - - +
108A GLN 3.1 2.2 - - - -
109A ASP* 3.0 31.9 + - - +
110A TYR* 3.8 15.9 - - - +
289A PHE* 3.6 26.0 - - + -
292A LYS* 4.0 44.6 - - + +
293A VAL* 4.1 10.3 - - + +
296A LYS* 4.6 6.7 - - + -
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 2.8 23.1 + - - +
104A ALA* 3.3 4.2 + - - -
106A VAL* 1.3 71.7 - - - +
108A GLN* 1.3 59.7 + - - +
109A ASP 3.1 0.2 - - - -
110A TYR* 2.8 34.2 + - + +
112A LEU* 3.1 39.4 + - - +
180A HIS 5.2 0.3 + - - -
183A LYS* 4.0 38.2 - - + +
184A SER* 4.3 6.3 - - - +
185A GLN* 5.6 0.2 - - - +
289A PHE* 4.0 20.9 - - + -
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Residues in contact with GLN 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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104A ALA 3.3 8.7 + - - +
105A GLU* 3.5 31.6 + - - +
106A VAL 3.1 0.2 - - - -
107A THR* 1.3 75.9 + - - +
109A ASP* 1.3 64.8 + - - +
110A TYR 3.1 0.9 + - - -
111A GLY* 3.1 12.5 + - - -
112A LEU* 3.8 18.3 + - - +
114A PRO* 3.6 29.0 - - + +
117A ALA* 3.4 29.0 - - + +
118A ASN* 5.0 1.6 + - - +
121A MET* 4.4 9.1 - - - +
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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