Contacts of the strand formed by residues 92 - 106 (chain A) in PDB entry 3KJO
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 GLU 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A VAL* 4.1 1.6 - - - -
89A TYR* 2.6 41.1 + - - +
90A LYS* 2.8 10.7 + - + +
91A LYS* 1.3 91.6 + - + +
93A THR* 1.3 70.4 + - - +
94A GLN* 3.6 1.1 + - + +
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Residues in contact with THR 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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17A LEU* 5.0 9.6 - - + +
18A LYS* 6.1 0.2 - - - -
19A GLY 5.6 1.8 - - - +
57A LEU* 4.3 18.7 - - + +
58A THR* 4.8 4.7 + - - +
86A ILE* 3.7 28.3 - - + -
87A GLN 3.4 7.0 - - - +
88A VAL* 4.3 12.0 - - + +
91A LYS 3.9 3.1 + - - -
92A GLU* 1.3 84.0 + - - +
94A GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 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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57A LEU* 4.2 6.5 - - - -
58A THR* 3.5 16.3 - - + +
60A LEU* 3.3 30.0 - - + +
86A ILE* 3.8 2.2 - - - -
87A GLN* 2.8 75.3 + - + +
89A TYR* 3.5 29.8 - - + +
92A GLU* 4.5 1.3 - - + +
93A THR* 1.3 77.8 - - - +
95A GLY* 1.3 60.6 + - - +
96A ILE* 4.7 5.1 - - - +
6B G 3.0 23.8 + - - +
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Residues in contact with GLY 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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57A LEU* 4.0 3.7 - - - +
58A THR 2.8 13.0 + - - +
59A CYS* 3.9 9.6 - - - -
60A LEU* 2.7 35.5 + - - +
84A LEU* 4.1 11.4 - - - -
85A LYS 3.4 8.1 - - - -
86A ILE* 4.3 8.5 - - - -
94A GLN* 1.3 74.9 - - - +
96A ILE* 1.3 57.3 + - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.1 15.9 - - + +
62A PHE* 4.2 20.4 - - + -
84A LEU* 3.4 10.1 - - - +
85A LYS* 2.9 55.8 + - + +
87A GLN* 3.7 40.2 - - - +
94A GLN* 4.7 3.6 - - - +
95A GLY* 1.3 75.7 - - - +
97A THR* 1.3 75.4 + - - +
4B U 5.9 2.0 - - + +
5B A 4.5 11.9 - - + +
6B G 4.6 2.9 - - - +
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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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60A LEU 3.2 5.6 + - - -
61A LEU* 3.5 23.8 - - + +
62A PHE* 3.0 53.6 + - - +
69A LEU* 5.0 1.3 - - + -
85A LYS* 4.7 1.4 - - - +
96A ILE* 1.3 87.6 - - - +
98A SER* 1.3 59.8 + - - +
101A PHE* 3.7 30.1 - - + -
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Residues in contact with SER 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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22A ILE* 3.2 28.1 - - - +
83A ARG* 3.2 24.6 + - - -
85A LYS* 4.0 20.5 - - - +
97A THR* 1.3 75.7 - - - +
99A SER* 1.3 73.7 + - - +
100A GLY 3.4 0.2 + - - -
101A PHE* 3.0 18.5 + - - +
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Residues in contact with SER 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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83A ARG* 3.5 15.8 - - - +
98A SER* 1.3 81.8 + - - +
100A GLY* 1.3 60.6 + - - +
101A PHE 3.3 0.3 + - - -
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Residues in contact with GLY 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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83A ARG* 3.0 32.5 + - - -
98A SER 3.4 0.2 + - - -
99A SER* 1.3 73.7 - - - +
101A PHE* 1.3 68.8 + - - +
102A ALA* 3.9 1.6 - - - +
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Residues in contact with PHE 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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61A LEU* 3.8 15.0 - - + -
68A ALA* 4.6 13.2 - - - +
69A LEU* 5.4 2.0 - - + -
70A PRO* 4.3 14.4 - - + -
81A PHE* 3.6 36.1 - + + -
82A HIS 3.3 20.2 - - - -
83A ARG* 3.5 14.1 - - - +
84A LEU* 3.9 24.0 - - + -
97A THR* 3.7 28.9 - - + -
98A SER 3.0 19.2 + - - +
99A SER 3.2 0.8 + - - -
100A GLY* 1.3 78.2 - - - +
102A ALA* 1.3 64.8 + - - +
103A SER* 4.1 13.5 - - - -
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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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68A ALA 5.6 1.8 - - - -
80A ARG 3.8 0.2 - - - +
81A PHE* 3.6 1.0 - - - -
82A HIS* 2.8 41.5 + - + +
83A ARG* 4.0 13.2 - - - +
100A GLY 3.3 6.3 + - - +
101A PHE* 1.3 83.5 - - - +
103A SER* 1.3 63.8 + - - +
120A SER* 4.1 18.4 - - - +
123A PHE* 6.4 1.8 - - + -
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Residues in contact with SER 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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68A ALA 4.9 3.3 + - - -
69A LEU 4.4 1.7 + - - -
70A PRO* 3.3 31.5 - - - +
71A ILE 4.6 0.5 + - - -
80A ARG* 3.1 11.9 - - - +
81A PHE* 3.5 24.2 - - - -
101A PHE* 4.1 5.0 - - - -
102A ALA* 1.3 77.2 - - - +
104A LEU* 1.3 65.7 + - - +
105A THR* 4.7 0.9 + - - -
117A ARG 3.9 1.6 + - - +
118A THR* 2.9 29.1 + - - -
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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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78A ILE 3.9 0.2 - - - +
79A VAL* 3.2 4.7 - - - +
80A ARG* 2.9 76.6 + - + +
103A SER* 1.3 76.1 - - - +
105A THR* 1.3 64.1 + - - +
106A PHE* 3.9 28.2 - - + -
116A PRO* 3.9 10.1 - - + -
117A ARG 3.5 1.8 - - - +
118A THR* 3.4 32.5 - - + +
123A PHE* 3.8 23.1 - - + -
124A ASN 4.0 5.2 - - - +
125A PHE* 4.2 7.9 - - + -
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Residues in contact with THR 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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70A PRO* 4.3 3.8 - - - +
71A ILE 3.3 33.0 + - - +
72A ILE* 4.1 3.4 - - - +
77A ASP* 3.9 16.2 - - + +
78A ILE 3.3 9.0 - - - +
79A VAL* 3.6 15.9 - - + +
103A SER* 4.7 0.3 + - - -
104A LEU* 1.3 76.6 - - - +
106A PHE* 1.3 67.3 + - - +
115A ILE 3.5 2.1 - - - +
117A ARG* 2.8 71.6 + - - +
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Residues in contact with PHE 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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26A TYR* 4.2 17.3 - + - -
77A ASP* 3.5 8.1 - - - +
78A ILE* 2.8 47.6 + - + +
80A ARG* 4.5 0.4 - - + -
104A LEU* 3.9 34.8 - - + -
105A THR* 1.3 74.0 - - - +
107A GLU* 1.3 67.1 + - - +
114A ILE* 3.8 22.2 - - + -
115A ILE 4.0 7.6 - - - +
116A PRO* 3.6 31.2 - - + -
117A ARG* 4.1 7.9 - - - +
125A PHE* 3.7 25.4 - + - -
133A VAL* 3.8 28.5 - - + -
137A ARG* 4.6 3.4 - - - +
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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