Contacts of the helix formed by residues 80 - 96 (chain A) in PDB entry 4KMR
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 GLN 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PRO* 4.0 12.2 - - - +
77A GLU* 3.0 45.4 + - + +
78A LEU 3.0 3.3 - - - +
79A GLY* 1.3 77.5 - - - +
81A ALA* 1.3 67.4 + - - +
82A PHE* 3.2 3.4 - - + +
83A PHE* 3.0 36.2 + - + +
84A ALA 3.0 18.7 + - - -
133A LEU* 5.2 4.7 - - - +
258A ASP* 5.5 4.3 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 5.0 0.2 - - - -
79A GLY 3.6 4.9 + - - -
80A GLN* 1.3 70.5 - - - +
82A PHE* 1.3 63.2 + - - +
84A ALA* 4.4 6.5 - - - -
85A GLN* 2.9 33.8 + - - +
232A ARG* 6.2 0.9 - - - +
258A ASP* 4.7 14.7 + - - +
286A VAL* 3.9 30.7 - - + +
287A ALA* 5.8 0.7 - - - -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.2 2.6 - - + +
81A ALA* 1.3 78.9 - - - +
83A PHE* 1.3 94.0 + + + +
85A GLN* 3.9 1.6 - - - +
86A LEU* 3.0 42.6 + - + +
166A MSE 4.0 25.8 - - - -
256A ASN* 6.3 0.7 - - - +
258A ASP* 5.4 1.4 + - - -
284A ASP* 3.6 37.2 - - + +
286A VAL* 4.0 12.4 - - + +
301A PRO* 4.6 2.0 - - + -
303A ARG* 3.9 31.2 - - + -
306A ILE* 5.5 3.6 - - + -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.8 30.2 - - + +
76A PRO* 3.7 24.2 - - + -
77A GLU 3.6 17.5 - - - +
78A LEU* 4.2 2.9 - - - +
80A GLN* 3.0 36.7 + - + +
82A PHE* 1.3 102.1 - + + +
84A ALA* 1.3 60.8 + - - +
86A LEU* 3.8 9.6 - - + +
87A ALA* 2.9 30.7 + - - +
131A ALA* 3.7 24.7 - - + -
133A LEU* 4.7 12.6 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.3 34.4 + - + +
80A GLN 3.0 9.8 + - - +
81A ALA* 3.8 8.3 - - - +
83A PHE* 1.3 75.5 - - - +
85A GLN* 1.3 61.1 + - + +
87A ALA* 3.4 1.2 + - - +
88A ASP* 3.0 23.4 + - - +
78B LEU* 3.5 35.2 - - + +
84B ALA* 3.8 8.3 - - + -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 2.9 20.6 + - - +
82A PHE 4.0 0.7 - - - +
84A ALA* 1.3 76.4 - - + +
86A LEU* 1.3 63.6 + - - +
88A ASP* 3.4 8.3 + - - +
89A GLU* 3.1 27.5 + - - +
285A ASP 4.0 1.4 - - - +
286A VAL* 2.9 53.1 + - + +
288A ASP 5.6 0.2 - - - +
303A ARG* 3.6 23.2 + - - +
79B GLY* 4.2 26.5 + - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 5.5 2.5 - - + -
75A VAL* 5.5 3.1 - - + -
82A PHE* 3.0 39.0 + - + +
83A PHE* 3.8 16.2 - - + +
85A GLN* 1.3 78.0 - - - +
87A ALA* 1.3 57.5 + - - +
89A GLU* 3.1 4.1 + - + -
90A VAL* 2.9 41.8 + - + +
152A LEU* 4.0 28.7 - - + -
303A ARG* 3.8 29.1 - - + +
306A ILE* 4.1 25.1 - - + -
307A ALA* 4.6 3.1 - - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.7 27.3 - - + +
75A VAL* 5.7 0.4 - - + -
78A LEU* 4.0 11.0 - - + -
83A PHE 2.9 18.9 + - - +
84A ALA 3.6 4.5 - - - +
86A LEU* 1.3 77.4 - - - +
88A ASP* 1.3 58.1 + - - +
90A VAL* 3.3 0.9 + - - +
91A ILE* 2.8 39.3 + - + +
103A VAL* 5.2 2.9 - - + -
78B LEU* 3.7 17.7 - - + -
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.0 14.3 + - - +
85A GLN* 3.5 12.9 - - - +
86A LEU 3.3 0.2 - - - -
87A ALA* 1.3 75.2 - - - +
89A GLU* 1.4 66.5 + - - +
91A ILE* 4.7 0.7 - - - -
92A ARG* 2.4 56.5 + - - +
77B GLU* 3.8 13.7 - - - +
78B LEU* 4.3 4.2 - - + +
79B GLY* 3.5 19.7 + - - +
105B GLN* 3.0 32.9 + - - +
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Residues in contact with GLU 89 (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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85A GLN 3.1 14.0 + - - +
86A LEU* 3.1 8.1 + - - +
88A ASP* 1.4 78.7 - - - +
90A VAL* 1.3 58.8 + - - +
92A ARG* 3.3 21.4 + - - +
93A VAL* 3.0 37.2 + - + +
303A ARG* 4.3 22.0 + - + +
304A HIS* 3.0 44.5 + - + -
307A ALA* 3.7 18.4 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.5 3.6 - - + -
73A LEU* 4.3 20.0 - - + -
86A LEU* 2.9 33.8 + - + +
87A ALA 3.7 4.9 - - - +
89A GLU* 1.3 71.6 - - - +
91A ILE* 1.3 58.5 + - - +
93A VAL* 4.0 0.5 - - - +
94A ALA* 2.8 33.4 + - - +
101A VAL* 4.4 16.2 - - + -
129A LEU* 3.8 31.9 - - + -
152A LEU* 5.5 2.9 - - + -
307A ALA* 4.0 21.5 - - + -
310A ALA* 5.7 1.1 - - + -
311A VAL* 4.1 10.8 - - + +
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Residues in contact with ILE 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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73A LEU* 5.9 0.4 - - + -
87A ALA* 2.8 28.8 + - + +
88A ASP 3.8 3.6 - - - +
90A VAL* 1.3 72.2 - - + +
92A ARG* 1.3 59.1 + - - +
94A ALA* 3.4 1.4 + - - +
95A ALA* 3.0 31.2 + - + +
99A LEU 5.1 0.3 - - - +
101A VAL* 4.0 29.8 - - + +
103A VAL* 4.8 4.7 - - + -
78B LEU* 3.8 25.1 - - + -
103B VAL* 3.7 33.4 - - + +
104B GLU* 4.5 5.4 - - + -
105B GLN* 3.9 24.7 - - + +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 2.4 45.7 + - - +
89A GLU* 3.8 19.6 + - - +
91A ILE* 1.3 80.0 - - - +
93A VAL* 1.3 64.0 + - + +
95A ALA* 3.4 12.7 + - - +
96A GLU* 3.5 21.6 + - - +
77B GLU* 5.5 6.5 + - - +
105B GLN* 4.4 13.8 - - - +
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Residues in contact with VAL 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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89A GLU* 3.0 21.8 + - + +
90A VAL 4.0 2.5 - - - +
92A ARG* 1.3 74.2 - - + +
94A ALA* 1.3 68.1 + - - +
96A GLU* 3.0 25.3 + - - +
97A GLN* 3.9 6.0 + - - +
304A HIS* 5.1 2.0 - - - +
307A ALA* 4.4 12.3 - - + +
308A ARG* 4.1 46.7 - - + +
311A VAL* 4.0 26.5 - - + -
312A THR* 5.7 1.1 - - - +
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Residues in contact with ALA 94 (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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71A ILE* 4.2 12.3 - - + -
90A VAL 2.8 19.4 + - - +
91A ILE 3.8 3.1 - - - +
93A VAL* 1.3 77.6 - - - +
95A ALA* 1.3 61.5 - - - +
97A GLN* 3.0 12.8 + - - +
99A LEU* 3.0 39.7 + - + +
101A VAL* 3.9 20.4 - - + -
311A VAL* 4.3 12.5 - - + +
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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 ILE* 3.0 20.2 + - + +
92A ARG* 3.7 7.9 - - - +
93A VAL 3.1 0.6 - - - -
94A ALA* 1.3 77.5 - - - +
96A GLU* 1.3 60.9 + - - +
97A GLN 3.1 1.1 + - - -
98A ASP* 3.3 13.7 + - - +
99A LEU 3.7 10.5 + - - +
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Residues in contact with GLU 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 ARG* 3.5 21.6 - - + +
93A VAL* 3.0 12.6 + - + +
95A ALA* 1.3 77.0 - - - +
97A GLN* 1.3 57.1 + - - +
98A ASP* 3.5 1.0 + - - +
308A ARG* 3.1 30.5 + - - +
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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