Contacts of the helix formed by residues 74 - 93 (chain A) in PDB entry 3PEJ
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 SER 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 1.4 75.0 - - - +
75A HIS* 1.3 60.6 + - - +
76A GLN* 3.6 18.2 + - - +
77A TYR* 3.5 16.5 + - - +
78A GLN* 3.2 26.4 + - - +
166A ALA* 5.3 2.7 - - - +
226A PHE* 4.0 7.7 - - - -
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 4.5 0.2 + - - -
74A SER* 1.3 71.5 + - - +
76A GLN* 1.4 65.1 + - - +
78A GLN* 3.3 14.3 + - + +
79A THR* 2.9 46.1 + - + -
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.4 11.0 + - - +
75A HIS* 1.4 80.5 + - - +
77A TYR* 1.4 55.1 + - - +
79A THR* 3.5 6.1 + - - -
80A GLU* 3.1 29.5 + - - +
166A ALA* 3.3 22.8 - - + +
167A LYS* 3.3 32.0 - - - +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.5 18.2 + - - +
75A HIS 3.3 0.4 - - - -
76A GLN* 1.4 76.5 - - - +
78A GLN* 1.3 60.2 + - + +
80A GLU* 3.4 0.6 + - - -
81A VAL* 2.9 58.9 + - + +
162A LEU* 3.4 53.0 - - + +
165A ILE* 4.2 6.1 - - + -
166A ALA* 3.7 17.1 - - + +
195A TYR* 2.7 33.6 + - - -
218A TRP* 3.7 10.0 + - - -
220A SER* 4.8 2.5 + - - -
224A ALA 4.1 11.4 - - - -
226A PHE* 3.5 38.1 - + + -
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 5.4 8.7 - - - +
74A SER 3.2 11.9 + - - +
75A HIS* 3.3 18.6 + - + +
77A TYR* 1.3 78.5 - - + +
79A THR* 1.3 55.1 + - - +
82A THR* 2.5 34.1 + - - +
223A ASP 4.1 8.8 + - - +
224A ALA* 3.3 35.6 + - + +
225A LYS* 3.9 17.2 - - - +
226A PHE* 6.1 0.2 - - - -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 2.9 35.9 + - - -
76A GLN* 3.9 5.6 - - - -
78A GLN* 1.3 75.2 - - - +
80A GLU* 1.4 64.0 + - - +
82A THR* 3.5 5.5 + - - -
83A ARG* 3.2 35.7 + - + +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN 3.1 18.9 + - - +
77A TYR* 3.4 2.9 + - - +
79A THR* 1.4 73.0 - - - +
81A VAL* 1.3 54.6 + - - +
83A ARG* 3.1 10.4 + - - +
84A LEU* 2.8 51.6 + - + +
165A ILE* 3.4 26.1 - - + +
166A ALA* 4.1 11.3 - - - +
169A GLY* 3.5 12.7 - - - -
170A THR* 3.0 16.3 + - - -
171A SER* 2.6 48.2 + - - -
192A VAL* 5.5 0.2 - - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 2.9 59.4 + - + +
80A GLU* 1.3 67.9 - - + +
82A THR* 1.4 56.4 + - - +
84A LEU* 3.2 7.1 + - + +
85A MET* 2.8 61.7 + - + +
165A ILE* 4.2 9.2 - - + -
195A TYR* 3.7 26.9 - - + -
224A ALA* 3.9 13.7 - - + -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 2.5 29.1 + - - +
79A THR* 3.6 6.7 - - - -
80A GLU 3.3 0.6 - - - -
81A VAL* 1.4 75.4 - - - +
83A ARG* 1.3 57.5 + - + +
85A MET* 3.7 6.3 - - - +
86A ASP* 2.9 52.2 + - - +
223A ASP* 4.5 4.4 + - - -
224A ALA* 3.2 14.4 + - - +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.2 27.2 + - + +
80A GLU* 3.1 10.8 + - - +
82A THR* 1.3 74.4 - - + +
84A LEU* 1.4 64.0 + - - +
86A ASP* 3.1 8.8 + - - +
87A ILE* 2.9 39.1 + - + +
171A SER* 3.0 31.0 + - - -
172A ASN* 2.6 36.1 + - - +
175A GLU* 2.8 31.3 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 2.8 38.7 + - + +
81A VAL* 3.5 15.7 - - + +
83A ARG* 1.4 71.1 - - - +
85A MET* 1.3 56.1 + - - +
87A ILE* 3.4 2.5 + - - +
88A ILE* 2.9 37.9 + - + +
165A ILE* 4.2 11.9 - - + -
170A THR 4.2 1.1 - - - -
171A SER* 3.7 25.6 - - - +
174A LEU* 3.8 23.3 - - + -
192A VAL* 3.8 33.2 - - + -
195A TYR* 4.2 20.6 - - + -
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 2.8 45.1 + - + +
82A THR* 3.7 6.1 - - - +
84A LEU* 1.3 72.2 - - - +
86A ASP* 1.4 59.4 + - - +
88A ILE* 4.6 3.8 - - - -
89A VAL* 2.9 40.1 + - + +
195A TYR* 4.5 11.9 - - + +
198A PHE* 3.5 48.5 - - + -
220A SER* 5.7 1.3 - - - -
221A THR 3.4 23.1 - - - +
222A ALA* 3.3 25.6 - - - +
224A ALA* 4.2 4.9 - - - -
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 2.9 44.2 + - - +
83A ARG* 3.5 8.5 - - - +
85A MET* 1.4 75.7 - - - +
87A ILE* 1.4 55.0 + - + +
89A VAL* 4.0 3.4 - - - +
90A ASN* 2.9 36.7 + - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 2.9 38.3 + - + +
84A LEU* 4.0 2.0 - - - +
86A ASP* 1.4 71.0 - - + +
88A ILE* 1.4 55.5 + - - +
90A ASN* 3.3 5.9 + - - +
91A SER* 2.9 39.5 + - - -
171A SER* 3.4 33.0 - - - +
174A LEU* 3.8 32.8 - - + +
175A GLU* 3.8 17.7 - - + +
178A SER* 4.2 12.1 - - - +
184A MET* 4.0 12.8 - - + -
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Residues in contact with ILE 88 (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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84A LEU* 2.9 23.8 + - + +
85A MET* 4.0 2.9 - - - +
87A ILE* 1.4 73.2 - - - +
89A VAL* 1.3 59.5 + - + +
91A SER 3.8 0.2 - - - -
92A LEU* 2.9 43.1 + - + +
174A LEU* 4.1 12.1 - - + -
184A MET* 4.5 9.2 - - + -
187A ILE* 4.1 29.4 - - + -
192A VAL* 5.4 5.8 - - + +
195A TYR* 4.5 5.8 - - + +
196A SER* 3.8 36.3 - - - +
199A LEU* 4.3 7.4 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 2.9 25.9 + - + +
86A ASP* 4.1 3.4 - - - +
88A ILE* 1.3 77.1 - - + +
90A ASN* 1.4 61.2 + - - +
93A TYR* 3.1 33.2 + - + +
96A LYS* 5.8 3.4 - - - -
195A TYR 5.7 0.2 - - - +
198A PHE* 3.6 33.0 - - + +
199A LEU* 3.7 18.4 - - + +
248A LYS* 5.4 6.3 - - - +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP 2.9 24.6 + - - +
87A ILE* 3.7 5.4 - - - +
89A VAL* 1.4 73.1 - - - +
91A SER* 1.3 57.4 + - - +
93A TYR* 3.2 30.8 - - - -
178A SER* 4.4 12.3 + - - -
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Residues in contact with SER 91 (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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87A ILE 2.9 18.0 + - - -
88A ILE 4.0 0.2 - - - -
90A ASN* 1.3 78.8 + - - +
92A LEU* 1.3 59.7 + - - +
93A TYR* 3.7 1.0 + - - -
94A THR* 4.4 4.2 + - - -
95A GLN* 3.9 13.3 + - - -
178A SER* 3.0 25.5 + - - -
182A GLY 5.5 1.4 + - - -
184A MET* 3.6 31.7 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 2.9 31.1 + - + +
91A SER* 1.3 78.5 - - - +
93A TYR* 1.4 55.7 + - - +
94A THR 3.1 5.4 - - - -
95A GLN* 2.9 32.9 + - + +
96A LYS* 2.9 27.2 + - - -
98A VAL* 3.9 29.8 - - + -
101A ARG* 6.1 1.1 - - - +
184A MET* 3.7 35.2 - - + +
187A ILE* 4.5 10.5 - - + -
199A LEU* 3.6 16.2 - - + -
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.1 19.5 + - + +
90A ASN* 3.2 34.8 - - - -
91A SER 3.7 1.5 - - - -
92A LEU* 1.4 74.7 - - - +
94A THR* 1.3 78.3 + - + +
95A GLN 3.4 0.2 - - - -
96A LYS* 3.4 41.8 + - - +
199A LEU* 4.0 1.8 - - + -
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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