Contacts of the strand formed by residues 84 - 99 (chain H) in PDB entry 1KN0
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 TRP 84 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26H PHE* 3.8 2.2 - - - -
72H ILE* 4.4 11.9 - - + -
75H ALA* 3.8 26.9 - - + -
76H ASN* 3.2 23.0 + - - +
79H PHE* 3.7 20.0 - + + -
80H GLY 3.6 15.9 + - - -
81H TYR 4.2 3.1 + - - +
82H ASN 3.5 0.4 - - - -
83H GLY* 1.3 80.3 - - - +
85H ALA* 1.3 72.1 + - - +
86H HIS* 4.3 4.3 - + - -
113H VAL* 3.8 16.8 - - + -
114H GLN 3.3 7.6 - - - +
115H LEU* 4.0 8.5 - - + -
151H LEU* 3.9 37.2 - - + -
155H LEU* 4.2 12.3 - - + -
119I SER* 3.9 11.8 + - - -
121I HIS* 3.2 41.0 + + - -
157I SER* 3.7 19.3 - - - -
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H PHE* 3.7 15.9 - - + -
84H TRP* 1.3 79.4 - - - +
86H HIS* 1.3 59.0 + - - +
113H VAL* 3.1 6.6 - - - +
114H GLN* 2.6 37.4 + - - +
120I TYR* 2.7 51.8 - - + +
121I HIS* 4.0 4.5 - - - -
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Residues in contact with HIS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H TRP* 4.3 4.7 - + + -
85H ALA* 1.3 77.4 - - - +
87H SER* 1.3 61.3 + - - +
88H ILE* 5.7 0.4 - - + +
111H VAL* 3.9 20.1 - - + +
112H ARG 3.0 13.2 - - - +
113H VAL* 4.1 11.0 - - + -
147H VAL* 5.2 5.4 - - + +
151H LEU* 3.7 30.8 - - + +
120I TYR* 3.2 14.9 + - - -
121I HIS* 2.9 39.5 - + - +
122I GLU 3.1 40.8 + - - -
123I ASP* 4.6 8.5 - - - +
157I SER* 3.5 20.2 + - - -
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Residues in contact with SER 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 1.3 79.0 - - - +
88H ILE* 1.3 66.4 + - - +
89H THR* 3.5 3.1 + - - -
111H VAL* 3.4 6.6 - - - +
112H ARG* 3.0 41.7 + - - +
112I ARG* 4.9 7.6 - - - -
120I TYR* 3.9 17.8 + - - -
122I GLU* 3.4 17.0 - - - -
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Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H HIS* 5.7 0.4 - - - +
87H SER* 1.3 73.6 + - - +
89H THR* 1.3 67.2 + - - +
90H GLN* 3.8 23.5 - - - +
91H GLN* 4.4 3.6 - - + -
109H ALA* 5.0 2.7 - - + -
110H PHE 3.6 7.2 - - - +
111H VAL* 4.7 5.8 - - + +
147H VAL* 3.7 34.8 - - + -
89I THR* 5.8 1.6 - - - +
110I PHE* 3.7 35.2 - - + -
122I GLU* 2.6 33.9 + - + +
123I ASP* 3.7 26.9 - - - +
124I VAL 3.9 0.2 - - - +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ILE 5.7 2.2 - - - +
87H SER* 3.5 5.6 + - - -
88H ILE* 1.3 74.4 - - - +
90H GLN* 1.3 68.3 + - + +
110H PHE* 2.8 16.9 + - + -
112H ARG* 4.0 16.1 + - - +
122H GLU* 2.6 29.3 + - - +
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Residues in contact with GLN 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 3.2 6.8 - - - -
89H THR* 1.3 89.6 - - + +
91H GLN* 1.3 71.3 + - - +
92H ASN* 4.6 9.2 - - + +
109H ALA* 3.3 1.9 - - - +
110H PHE* 2.7 54.7 + - + +
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Residues in contact with GLN 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 4.3 2.4 - - + +
90H GLN* 1.3 81.4 - - - +
92H ASN* 1.3 62.4 + - - +
93H VAL 4.2 0.7 + - - -
107H VAL* 3.7 14.1 - - + +
108H CYS 3.3 13.5 - - - +
109H ALA* 4.1 8.2 - - + +
143H ARG* 2.7 75.2 + - - +
147H VAL* 3.7 10.2 - - - +
110I PHE* 3.3 39.7 - - + -
124I VAL* 3.8 3.1 - - - +
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ARG* 4.5 6.5 - - - +
90H GLN* 4.2 12.3 - - + +
91H GLN* 1.3 75.0 - - - +
93H VAL* 1.3 72.7 + - - +
94H ASP* 3.3 26.1 + - - +
107H VAL* 4.2 1.8 - - - -
108H CYS* 3.0 44.7 + - - -
110H PHE* 5.7 2.0 - - + -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H GLN 4.2 0.4 + - - -
92H ASN* 1.3 80.3 + - - +
94H ASP* 1.3 63.6 + - - +
95H PHE* 3.9 8.7 - - - +
96H VAL* 3.8 28.9 - - + -
107H VAL* 3.9 21.8 - - + -
139H LEU* 4.2 7.9 - - + -
143H ARG* 3.3 42.8 - - - +
94I ASP* 5.1 1.1 - - - +
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Residues in contact with ASP 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 5.0 2.0 - - - +
139G LEU* 3.5 20.6 - - + +
143G ARG* 2.4 35.9 + - - -
92H ASN* 3.3 20.2 + - - +
93H VAL* 1.3 73.7 - - - +
95H PHE* 1.3 62.4 + - + +
106H GLY 2.8 19.5 + - - +
108H CYS* 4.7 0.2 - - - -
126H TYR* 2.6 33.8 + - - +
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Residues in contact with PHE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G LYS* 3.4 43.5 - - + +
136G ALA* 3.5 30.1 - - + -
139G LEU* 3.6 21.8 - - + -
93H VAL* 3.5 3.2 - - - +
94H ASP* 1.3 85.1 - - + +
96H VAL* 1.3 72.1 + - - +
97H ASP* 3.4 19.1 - - - +
104H TYR* 3.0 33.0 - - + -
105H VAL* 3.5 3.5 - - - +
106H GLY* 3.3 36.6 + - - +
130H GLU* 5.7 0.4 - - - -
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Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H VAL* 3.8 19.7 - - + -
95H PHE* 1.3 82.1 - - - +
97H ASP* 1.3 62.5 + - - +
98H LEU* 4.2 0.9 + - - +
103H PHE* 4.2 13.0 - - + -
104H TYR 3.7 3.8 - - - -
105H VAL* 3.9 15.3 - - + -
135H LYS* 4.1 27.6 - - + -
139H LEU* 3.8 19.7 - - + -
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Residues in contact with ASP 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G LYS* 2.8 39.9 + - - -
95H PHE* 3.4 10.1 - - - +
96H VAL* 1.3 79.8 + - - +
98H LEU* 1.3 61.2 + - - +
99H ASN* 4.0 11.4 - - - +
102H LYS 3.8 0.2 - - - +
103H PHE* 3.4 9.4 - - - -
104H TYR* 2.8 48.0 + - + +
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Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H VAL 4.2 1.4 + - - +
97H ASP* 1.3 72.3 - - - +
99H ASN* 1.3 64.9 + - - +
100H ASN 3.9 1.9 + - - +
101H GLY* 3.7 16.6 - - - +
102H LYS 3.1 35.0 - - - +
103H PHE* 3.7 32.1 - - + -
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Residues in contact with ASN 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ASP* 4.0 10.3 - - - +
98H LEU* 1.3 75.5 - - - +
100H ASN* 1.3 86.9 + - - +
101H GLY 3.6 0.2 - - - -
102H LYS* 2.9 22.6 + - - +
104H TYR* 3.7 38.0 - - + +
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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