Contacts of the strand formed by residues 144 - 161 (chain F) in PDB entry 5HK5
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 PHE 144 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU* 3.0 33.2 - - + +
135F LEU 3.5 8.7 - - - +
136F GLU* 5.0 0.2 - - - +
137F CYS* 3.8 5.5 + - - -
140F LEU* 4.1 0.9 - - - +
142F PRO* 2.7 42.0 + - + +
143F PRO* 1.3 81.8 - - + +
145F ARG* 1.3 76.6 + - - +
146F ILE* 4.2 28.9 - - + -
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLU* 3.6 32.1 + - + -
87F CYS* 3.5 30.3 - - - -
133F VAL 3.7 1.4 - - - +
134F GLU* 3.6 3.5 - - - -
135F LEU* 3.4 32.6 + - + +
137F CYS* 3.6 2.7 - - - -
140F LEU* 4.0 27.4 - - + +
144F PHE* 1.3 82.4 - - - +
146F ILE* 1.3 67.2 + - - +
147F LYS* 4.4 3.3 - - + +
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Residues in contact with ILE 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ILE* 3.5 45.8 - - + -
133F VAL 3.6 3.1 - - - -
134F GLU* 4.4 11.2 - - + +
144F PHE* 4.2 23.8 - - + -
145F ARG* 1.3 77.3 + - - +
147F LYS* 1.3 71.8 + - - +
148F LYS* 5.1 1.1 - - + +
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Residues in contact with LYS 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F VAL* 3.6 28.5 - - + -
83F SER 2.9 28.9 + - - +
84F GLU* 3.0 30.1 + - + +
131F VAL 3.3 3.5 - - - +
132F ILE* 3.6 1.4 - - - -
133F VAL* 2.7 44.8 + - - +
135F LEU* 4.3 5.8 - - + -
145F ARG* 4.4 8.5 - - + +
146F ILE* 1.3 84.8 - - - +
148F LYS* 1.3 61.6 + - - +
149F ILE* 3.7 10.2 + - + -
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Residues in contact with LYS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ARG* 5.4 8.1 + - - +
109E HIS* 5.1 8.0 + - - +
130F SER* 2.9 33.2 + - - +
131F VAL 3.7 4.3 - - - +
132F ILE* 4.1 25.8 - - + +
146F ILE* 5.8 0.7 - - + -
147F LYS* 1.3 71.4 - - - +
149F ILE* 1.3 68.4 + - - +
150F GLN 4.3 0.7 + - - -
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Residues in contact with ILE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ARG 5.5 0.9 - - - +
109E HIS* 4.8 15.0 - - + +
80F GLN* 3.5 25.6 - - - +
82F VAL* 4.1 33.2 - - + -
92F ILE* 4.0 15.7 - - + -
94F ASN* 4.0 0.9 - - - +
129F THR 3.6 0.7 - - - +
130F SER* 3.4 5.4 - - - -
131F VAL* 2.9 38.0 + - + +
133F VAL* 4.2 17.9 - - + -
147F LYS* 4.3 13.2 - - + +
148F LYS* 1.3 83.5 - - - +
150F GLN* 1.3 75.8 + - - +
151F LYS* 3.6 4.4 + - + -
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Residues in contact with GLN 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E TYR* 4.2 14.0 + - - +
107E PRO* 4.0 12.5 - - + +
108E ARG* 3.0 65.8 + - + +
109E HIS* 6.0 1.4 - - - +
116E SER* 5.4 0.5 - - - -
94F ASN* 2.9 21.3 + - - -
128F VAL* 3.7 23.3 - - + +
129F THR 3.4 5.4 - - - +
130F SER* 4.8 3.8 - - - +
148F LYS 4.2 1.0 + - - -
149F ILE* 1.3 76.8 - - - +
151F LYS* 1.3 59.1 + - - +
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Residues in contact with LYS 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ILE* 5.2 3.8 - - + -
93F LEU 3.6 23.8 + - - +
94F ASN* 3.5 20.7 - - - +
95F ARG* 5.3 8.5 - - - +
128F VAL* 3.5 6.2 - - - +
129F THR* 2.7 51.7 + - - +
131F VAL* 3.6 29.8 - - + -
149F ILE* 4.4 6.3 - - + +
150F GLN* 1.3 78.1 - - - +
152F VAL* 1.3 66.9 + - - +
153F LYS* 3.4 35.0 + - - +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 3.5 34.5 - - + +
107E PRO* 3.6 18.2 - - + -
75F THR* 4.3 7.0 - - - +
94F ASN* 3.3 6.1 + - - +
95F ARG* 3.5 37.9 - - + +
97F CYS* 3.8 6.1 - - - -
125F PRO* 4.1 12.3 - - + -
127F ARG 4.0 4.3 - - - -
128F VAL* 4.9 3.8 - - + +
151F LYS* 1.3 74.4 + - - +
153F LYS* 1.3 65.3 + - - +
154F HIS 4.2 4.0 - - - +
155F CYS* 3.8 29.2 - - - -
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Residues in contact with LYS 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F THR* 4.1 17.7 + - - +
95F ARG* 4.4 5.9 + - - +
127F ARG* 3.2 15.8 + - + +
129F THR* 3.8 35.2 - - + +
131F VAL* 5.8 1.1 - - - -
151F LYS* 3.4 31.7 - - - +
152F VAL* 1.3 81.6 - - - +
154F HIS* 1.3 86.5 + - + +
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Residues in contact with HIS 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F THR* 5.0 4.5 - - + -
125F PRO* 3.3 8.8 - - - +
126F GLN* 2.9 52.5 + - + +
127F ARG* 3.7 9.1 + - - +
152F VAL* 4.2 0.3 - - - +
153F LYS* 1.3 96.2 + - + +
155F CYS* 1.3 65.7 + - - +
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Residues in contact with CYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F CYS* 3.4 30.3 + - - +
74F LYS 3.9 11.0 - - - +
75F THR* 4.0 11.8 - - - +
97F CYS* 2.0 54.3 - - + -
123F CYS* 4.0 0.4 - - - -
124F LYS 3.3 5.2 - - - +
126F GLN* 4.1 4.7 - - - +
152F VAL* 3.8 10.1 - - - -
154F HIS* 1.3 78.9 - - - +
156F ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F CYS* 3.3 12.8 - - - -
122F PHE 3.6 0.3 - - - +
124F LYS* 2.9 30.8 + - + +
126F GLN* 4.0 43.5 + - + +
155F CYS* 1.3 77.5 - - - +
157F CYS* 1.3 70.5 + - - +
158F MET* 3.6 27.1 + - + +
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Residues in contact with CYS 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ASP* 3.3 32.3 - - + +
72F TRP 3.8 3.6 - - - -
73F CYS* 3.6 18.0 - - - +
101F CYS* 2.0 55.9 - - + -
122F PHE 3.6 1.6 - - - -
156F ARG* 1.3 78.2 - - - +
158F MET* 1.3 71.7 + - - +
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Residues in contact with MET 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ALA* 3.2 4.2 - - - +
122F PHE* 3.0 51.8 + - + +
124F LYS* 4.3 13.5 - - + +
156F ARG* 4.2 35.9 - - - +
157F CYS* 1.3 82.2 - - - +
159F SER* 1.3 71.1 + - - +
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ASN 5.1 2.5 - - - -
119F SER* 4.7 11.0 - - - -
120F CYS 3.1 15.9 - - - -
121F ALA* 3.8 11.7 - - - -
122F PHE* 4.1 3.1 - - - -
158F MET* 1.3 84.6 - - - +
160F VAL* 1.3 70.7 + - - +
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Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E CYS* 5.4 2.0 - - - -
119F SER* 3.2 7.1 - - - -
120F CYS* 2.8 43.3 + - + +
122F PHE* 4.0 22.9 - - + -
159F SER* 1.3 79.3 - - - +
161F ASN* 1.3 63.0 - - - +
162F LEU* 4.4 19.3 - - + -
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Residues in contact with ASN 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F SER 5.0 0.4 + - - -
117F PHE* 3.5 38.0 - - + +
118F GLN 3.2 29.3 + - - +
160F VAL* 1.3 77.5 - - - +
162F LEU* 1.3 67.1 + - - +
163F SER* 4.1 14.3 - - - +
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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