Contacts of the helix formed by residues 94 - 109 (chain A) in PDB entry 3K9W
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 ASP 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 1.3 71.7 - - - +
95A PHE* 1.3 61.3 + - - +
96A GLU* 3.6 13.0 + - - +
97A TYR* 3.2 36.3 + - + +
98A GLU* 3.0 23.9 + - - +
171A SO4 3.0 19.4 + - - +
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Residues in contact with PHE 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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89A LEU* 3.8 26.2 - - + -
90A ARG 3.1 26.9 - - - -
91A ALA* 3.4 23.1 - - - -
92A VAL* 4.7 0.4 - - - -
93A SER* 3.0 27.3 + - - -
94A ASP* 1.3 69.4 + - - +
96A GLU* 1.3 66.9 + - - +
98A GLU* 4.4 3.8 - - - +
99A PHE* 3.0 61.7 + + + -
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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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94A ASP* 3.3 9.9 + - - +
95A PHE* 1.3 76.7 - - - +
97A TYR* 1.3 58.9 + - + +
99A PHE* 4.0 2.5 - - - +
100A GLN* 2.9 61.9 + - + +
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Residues in contact with TYR 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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41A LYS* 4.3 7.4 + - - -
87A ARG* 3.8 10.1 - - - -
94A ASP* 3.2 28.9 + - + +
96A GLU* 1.3 82.8 - - + +
98A GLU* 1.3 64.4 + - - +
100A GLN* 3.8 10.8 - - + +
101A MET* 3.0 34.1 + - + +
167A 4PS 2.9 54.5 + - - -
171A SO4 3.6 20.9 - - - -
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Residues in contact with GLU 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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87A ARG* 2.8 50.5 + - - +
88A GLY 4.2 10.0 - - - +
89A LEU* 3.9 23.6 - - + -
93A SER* 4.7 2.0 - - - -
94A ASP 3.0 21.2 + - - +
95A PHE 3.3 3.3 + - - +
97A TYR* 1.3 78.9 - - - +
99A PHE* 1.3 61.3 + - + +
101A MET* 3.5 7.7 + - - +
102A ALA* 3.0 28.1 + - - +
116A PHE* 3.7 18.4 - - + -
171A SO4 2.7 29.2 + - - +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.2 19.1 - - + -
95A PHE* 3.0 52.8 + + + +
96A GLU* 4.3 2.2 - - - +
98A GLU* 1.3 76.2 - - - +
100A GLN* 1.3 61.9 + - - +
102A ALA* 3.9 4.3 - - + +
103A GLY* 2.9 26.3 + - - -
106A ARG* 5.1 2.9 + - - -
116A PHE* 4.0 27.1 - + - -
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Residues in contact with GLN 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 GLU* 2.9 50.4 + - + +
97A TYR* 3.8 8.6 - - + +
99A PHE* 1.3 74.3 - - - +
101A MET* 1.3 60.3 + - - +
103A GLY* 3.3 1.1 + - - -
104A MET* 2.9 45.4 + - + +
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Residues in contact with MET 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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7A PRO* 4.3 3.4 - - + -
73A LEU* 4.0 17.3 - - + -
85A ILE* 4.2 8.1 - - + -
87A ARG* 3.5 52.9 - - + -
97A TYR* 3.0 26.3 + - + +
98A GLU* 3.8 7.4 - - - +
100A GLN* 1.3 78.1 - - - +
102A ALA* 1.3 58.8 + - - +
104A MET* 3.3 1.0 + - - +
105A ASN* 2.8 55.5 + - - +
114A THR* 5.6 2.9 - - + +
167A 4PS 4.1 33.2 - - + +
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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 GLU 3.0 18.3 + - - +
99A PHE* 3.9 6.3 - - + +
101A MET* 1.3 78.3 - - - +
103A GLY* 1.3 58.5 + - - +
105A ASN* 3.9 1.9 - - - +
106A ARG* 3.0 44.3 + - + +
114A THR* 4.0 37.5 + - + -
116A PHE* 4.2 10.3 - - + -
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Residues in contact with GLY 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 PHE 2.9 18.2 + - - -
100A GLN* 3.8 0.9 - - - -
102A ALA* 1.3 77.0 - - - +
104A MET* 1.3 58.1 + - - +
106A ARG* 3.1 45.4 + - - +
107A TYR* 3.5 16.2 + - - -
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Residues in contact with MET 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 GLN* 2.9 29.7 + - - +
101A MET* 4.0 2.0 - - - +
103A GLY* 1.3 74.4 - - - +
105A ASN* 1.3 66.3 + - - +
106A ARG 3.1 0.2 - - - -
107A TYR* 3.1 14.9 + - + +
108A LEU* 3.1 29.8 + - + +
167A 4PS 4.5 15.7 - - - -
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Residues in contact with ASN 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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73A LEU* 3.7 28.9 - - - +
74A LYS 5.1 1.6 + - - -
85A ILE* 4.3 18.0 - - + +
101A MET* 2.8 47.6 + - - +
102A ALA* 4.0 5.8 - - - +
104A MET* 1.3 73.5 - - - +
106A ARG* 1.4 52.5 + - - +
108A LEU* 3.5 14.5 - - - +
109A LEU* 2.6 47.5 + - + +
112A VAL 5.9 0.4 - - - -
114A THR* 4.8 3.3 + - - +
167A 4PS 3.4 18.6 - - - +
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Residues in contact with ARG 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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99A PHE 5.1 2.2 + - - -
102A ALA* 3.0 31.0 + - + +
103A GLY* 3.1 37.7 + - - +
105A ASN* 1.4 73.2 - - - +
107A TYR* 1.3 57.4 + - + +
109A LEU 4.1 7.0 - - - -
110A PRO* 3.3 26.2 - - - +
112A VAL 5.4 6.5 - - - +
114A THR* 6.0 3.4 - - - +
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Residues in contact with TYR 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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103A GLY 3.5 17.9 + - - -
104A MET* 3.1 15.5 + - + +
106A ARG* 1.3 79.8 - - + +
108A LEU* 1.3 67.9 + - + +
109A LEU 3.4 0.2 - - - -
110A PRO* 4.0 11.0 - - - +
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Residues in contact with LEU 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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72A LEU* 6.3 2.5 - - + -
74A LYS* 3.5 49.8 - - + +
78A ARG* 4.9 1.9 + - - -
104A MET* 3.1 18.4 + - + +
105A ASN* 3.2 25.3 + - - +
107A TYR* 1.3 82.8 - - + +
109A LEU* 1.3 61.5 + - + +
110A PRO* 3.8 4.5 - - - +
167A 4PS 4.9 12.8 - - - +
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Residues in contact with LEU 109 (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* 5.5 0.2 - - + -
74A LYS* 3.8 47.1 - - + +
77A VAL* 4.3 11.4 - - + -
78A ARG* 3.5 36.8 - - + +
85A ILE* 4.0 27.1 - - + -
105A ASN* 2.6 29.3 + - - +
106A ARG* 4.2 2.3 - - - +
108A LEU* 1.3 77.0 - - + +
110A PRO* 1.3 68.1 - - - +
111A ASP* 3.2 3.8 - - - -
112A VAL* 3.0 29.8 + - + +
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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
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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