Contacts of the helix formed by residues 89 - 105 (chain A) in PDB entry 5K9S
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 ASN 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A SER* 3.2 16.4 + - - +
88A ASN* 1.3 76.4 - - - +
90A LEU* 1.3 64.0 + - - +
91A GLU* 2.5 39.6 + - - +
92A SER* 3.6 20.9 + - - +
93A GLN* 3.2 22.0 + - - +
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Residues in contact with LEU 90 (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 ASN 3.4 5.3 + - - +
89A ASN* 1.3 74.8 + - - +
91A GLU* 1.3 61.3 + - - +
93A GLN* 3.3 21.0 + - - +
94A LEU* 3.1 22.3 + - - +
130A LYS* 3.9 29.4 - - + -
132A ASP* 4.3 8.3 - - - +
133A CYS* 4.1 30.7 - - + -
136A ILE* 4.8 7.0 - - + -
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Residues in contact with GLU 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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89A ASN* 2.5 21.7 + - - +
90A LEU* 1.3 73.6 - - - +
92A SER* 1.3 57.4 + - - +
94A LEU* 3.5 18.6 + - - +
95A GLN* 3.1 55.5 + - - +
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Residues in contact with SER 92 (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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76A TRP* 5.3 1.2 - - - -
84A GLY* 3.2 17.2 - - - +
87A SER* 3.7 20.0 - - - -
89A ASN* 3.4 19.5 + - - +
90A LEU 3.3 0.2 - - - -
91A GLU* 1.3 75.3 - - - +
93A GLN* 1.3 60.0 + - - +
95A GLN* 3.9 11.6 + - - +
96A ALA* 3.1 23.6 + - - +
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Residues in contact with GLN 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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84A GLY 3.5 10.3 - - - +
85A ILE* 3.1 29.2 + - - +
86A ASN 4.9 0.2 - - - -
87A SER 3.3 17.0 + - - +
88A ASN* 4.8 2.7 - - - +
89A ASN 3.2 12.4 + - - +
90A LEU* 3.4 33.1 - - - +
91A GLU 3.3 0.4 - - - -
92A SER* 1.3 76.2 - - - +
94A LEU* 1.3 58.5 + - - +
96A ALA* 3.3 2.3 + - - +
97A THR* 2.9 33.6 + - - -
127A PHE* 3.7 23.2 - - + -
130A LYS* 4.4 6.3 + - - +
136A ILE* 3.8 13.7 - - + -
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Residues in contact with LEU 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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90A LEU 3.1 12.7 + - - +
91A GLU* 3.7 25.8 - - - +
92A SER 3.4 0.2 - - - -
93A GLN* 1.3 76.7 - - - +
95A GLN* 1.3 62.8 + - + +
97A THR* 3.1 1.9 + - - -
98A GLN* 2.9 49.5 + - - +
133A CYS* 4.6 10.3 - - - -
135A PRO* 4.0 22.2 - - + +
136A ILE* 3.8 40.7 - - + +
139A GLU* 4.2 8.1 - - + -
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Residues in contact with GLN 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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76A TRP* 4.1 25.3 - - + -
91A GLU* 3.1 43.5 + - - +
92A SER* 4.2 9.0 + - - +
93A GLN 3.4 0.2 - - - -
94A LEU* 1.3 76.5 - - + +
96A ALA* 1.3 57.3 + - - +
98A GLN* 3.3 18.9 + - - +
99A ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 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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76A TRP* 3.9 17.7 - - + -
81A ILE* 3.6 14.1 - - - +
84A GLY* 3.6 6.1 - - - -
85A ILE* 3.6 34.1 - - + +
92A SER 3.1 20.6 + - - +
93A GLN 3.7 1.1 - - - +
95A GLN* 1.3 76.8 - - - +
97A THR* 1.3 58.8 + - - +
99A ALA* 3.4 3.1 + - - +
100A ALA* 3.0 26.7 + - - +
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Residues in contact with THR 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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85A ILE* 4.2 2.7 - - - +
93A GLN 2.9 17.0 + - - -
94A LEU 3.7 3.1 - - - -
96A ALA* 1.3 74.8 - - - +
98A GLN* 1.3 59.7 - - - +
100A ALA* 3.3 5.8 + - - +
101A ARG* 2.8 28.6 + - - +
124A PHE* 3.9 19.8 - - + -
127A PHE* 3.7 21.3 - - - -
136A ILE* 3.9 8.1 - - + +
139A GLU* 3.5 35.4 - - + +
140A SER* 3.8 13.0 - - - +
143A ALA* 5.2 0.9 - - + -
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Residues in contact with GLN 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 LEU* 2.9 41.5 + - - +
95A GLN* 3.5 22.6 - - - +
97A THR* 1.3 75.9 - - - +
99A ALA* 1.3 56.6 + - - +
101A ARG* 3.1 4.9 + - - +
102A LYS* 2.8 45.2 + - - +
135A PRO* 6.0 0.4 - - - +
139A GLU* 3.5 32.7 + - + +
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Residues in contact with ALA 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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74A VAL* 5.6 2.9 - - + -
76A TRP* 3.4 51.9 - - + +
81A ILE* 4.1 4.7 - - + -
95A GLN 3.0 10.8 + - - +
96A ALA 3.6 8.1 - - - +
97A THR 3.3 0.2 - - - -
98A GLN* 1.3 74.5 - - - +
100A ALA* 1.3 58.1 + - - +
102A LYS* 3.2 10.9 + - - +
103A LEU* 2.8 30.7 + - - +
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Residues in contact with ALA 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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81A ILE* 3.8 23.5 - - + +
96A ALA 3.0 14.0 + - - +
97A THR* 3.6 8.3 - - - +
99A ALA* 1.3 74.7 - - - +
101A ARG* 1.3 58.3 + - - +
103A LEU* 3.2 4.5 + - - +
104A LEU* 2.9 38.1 + - + +
115A ILE* 4.8 7.6 - - + -
124A PHE* 3.8 28.3 - - + -
143A ALA* 5.2 0.4 - - + -
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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 THR 2.8 12.6 + - - +
98A GLN* 3.1 3.7 + - - +
100A ALA* 1.3 74.5 - - - +
102A LYS* 1.3 86.1 + - - +
104A LEU* 3.1 7.0 + - - +
105A SER* 2.7 27.6 + - - +
138A PHE* 4.7 3.4 - - - -
139A GLU* 2.9 50.9 + - - +
142A TRP* 3.4 60.0 - - + -
143A ALA* 4.6 7.3 - - + +
21B ARG* 3.1 43.8 - - - +
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Residues in contact with LYS 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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74A VAL* 4.0 31.0 - - + +
98A GLN* 2.8 33.2 + - - +
99A ALA* 3.7 6.3 - - - +
101A ARG* 1.3 97.4 - - - +
103A LEU* 1.3 62.5 + - - +
104A LEU 3.2 0.5 + - - -
105A SER* 3.3 15.5 + - - -
106A ARG* 3.4 15.8 + - - +
21B ARG* 4.5 13.6 - - + +
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Residues in contact with LEU 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* 5.8 4.5 - - - -
76A TRP 4.1 19.7 - - - +
78A VAL* 4.3 15.0 - - + -
81A ILE* 3.7 26.0 - - + -
99A ALA 2.8 16.1 + - - +
100A ALA 3.5 5.8 - - - +
102A LYS* 1.3 77.8 - - - +
104A LEU* 1.3 58.5 + - + +
106A ARG* 3.0 60.7 + - - +
110A PRO* 4.0 0.5 - - - +
111A PRO* 3.3 35.6 - - + +
115A ILE* 4.4 6.3 - - + -
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Residues in contact with LEU 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 ALA* 2.9 22.0 + - + +
101A ARG* 3.1 5.6 + - - +
103A LEU* 1.3 76.3 - - + +
105A SER* 1.3 58.3 + - - +
106A ARG 3.6 1.3 - - - -
110A PRO* 3.5 25.9 - - + +
111A PRO* 4.5 4.5 - - + -
112A ILE* 4.1 27.6 - - + -
115A ILE* 4.0 28.9 - - + -
124A PHE* 5.0 0.4 - - + -
142A TRP* 6.4 0.2 - - + -
143A ALA* 3.6 38.4 - - + +
146A ASN* 2.9 28.6 + - + +
147A ILE* 3.9 18.4 - - + -
18B ARG* 4.6 0.7 - - - -
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Residues in contact with SER 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 2.7 20.5 + - - -
102A LYS 3.3 3.1 + - - -
104A LEU* 1.3 76.3 - - - +
106A ARG* 1.3 62.5 + - - +
107A GLU 3.7 0.7 + - - -
142A TRP* 3.8 10.9 - - - -
146A ASN* 3.6 7.6 - - - +
18B ARG* 5.2 1.1 - - - +
19B ARG 3.4 19.7 - - - -
20B ASN* 3.6 10.8 - - - +
21B ARG* 3.1 51.1 + - - +
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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
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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