Contacts of the strand formed by residues 117 - 136 (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 117 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PHE* 4.1 22.2 - + + -
105F TYR* 3.2 11.0 - - - -
106F ILE* 3.0 50.3 + - + +
115F ASP 5.3 0.7 - - - +
116F SER* 1.3 75.0 - - - +
118F GLN* 1.3 59.4 + - - +
119F SER* 3.7 32.1 - - - -
161F ASN* 3.5 35.0 - - + +
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E PHE* 3.8 14.0 - - + +
123E CYS 3.1 23.0 + - - -
124E LYS* 3.2 25.2 - - - +
125E PRO* 4.1 0.7 - - - +
103F SER* 3.9 1.0 + - - -
104F PHE 3.3 16.8 + - - -
105F TYR* 3.3 22.9 - - + -
116F SER* 4.3 1.0 + - - +
117F PHE* 1.3 74.7 - - - +
119F SER* 1.3 74.5 + - - +
120F CYS* 3.9 14.5 + - - -
160F VAL 3.8 0.2 - - - +
161F ASN* 3.2 26.2 + - - +
162F LEU* 3.7 16.3 + - + +
163F SER 5.8 0.8 - - - +
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E PHE* 3.7 1.6 - - - +
102F ASN 4.5 1.0 + - - -
103F SER* 2.8 30.8 + - - -
104F PHE* 2.9 42.1 + - - -
117F PHE* 3.7 22.5 - - - -
118F GLN* 1.3 83.7 + - - +
120F CYS* 1.3 58.1 + - - +
159F SER* 4.7 12.6 - - - -
160F VAL 3.2 10.5 - - - -
161F ASN* 5.4 0.2 - - - -
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Residues in contact with CYS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E CYS* 3.5 24.5 - - - -
121E ALA 3.7 4.3 - - - -
122E PHE* 4.1 17.9 - - + -
118F GLN* 4.0 11.0 - - - -
119F SER* 1.3 77.9 - - - +
121F ALA* 1.3 60.7 + - - +
122F PHE* 3.8 5.5 - - - -
159F SER* 3.1 2.8 - - - -
160F VAL* 2.8 36.8 + - + +
162F LEU* 3.6 42.6 - - + -
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E CYS 5.5 0.5 - - - +
103E SER* 4.1 2.8 + - - -
121E ALA* 2.9 37.1 + - - +
101F CYS* 3.6 19.7 - - + +
102F ASN 3.3 26.5 - - - +
103F SER* 4.8 1.8 - - - -
119F SER 4.4 0.2 + - - -
120F CYS* 1.3 73.9 - - - +
122F PHE* 1.3 64.9 + - - +
157F CYS* 5.6 0.2 - - + -
158F MET 3.2 12.8 - - - +
159F SER* 3.8 8.1 - - - +
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Residues in contact with PHE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E SER* 3.2 5.6 - - - -
118E GLN* 3.7 11.9 - - + +
119E SER 3.4 20.0 - - - +
120E CYS* 3.5 28.9 - - + -
101F CYS* 4.0 5.7 - - - -
120F CYS 3.8 13.0 - - - -
121F ALA* 1.3 75.7 - - - +
123F CYS* 1.3 62.0 + - - +
124F LYS* 3.3 27.4 + - + -
156F ARG 3.6 0.3 - - - +
158F MET* 3.0 43.1 + - + -
159F SER* 4.1 6.3 - - - -
160F VAL* 4.0 27.6 - - + -
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Residues in contact with CYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E SER* 3.0 14.7 + - - +
104E PHE 3.9 2.3 - - - -
105E TYR 3.9 5.9 + - - -
118E GLN* 3.2 12.4 + - - -
73F CYS* 2.1 50.0 - - + -
97F CYS* 3.6 22.9 - - - +
98F TYR 3.5 8.7 - - - -
99F GLY* 3.5 32.8 - - - +
101F CYS* 3.8 8.6 - - - -
122F PHE* 1.3 68.9 - - - +
124F LYS* 1.3 57.3 + - - +
155F CYS* 4.0 0.9 - - - -
156F ARG 3.8 1.3 - - - -
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Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 4.3 0.2 - - - -
118E GLN* 2.9 26.7 - - - +
97F CYS* 3.7 6.1 - - - -
122F PHE* 3.7 32.2 - - + +
123F CYS* 1.3 73.0 - - - +
125F PRO* 1.3 87.0 - - + +
126F GLN* 3.3 0.6 + - - +
155F CYS* 3.3 0.5 - - - -
156F ARG* 2.9 38.9 + - + +
158F MET* 4.3 13.2 - - + +
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Residues in contact with PRO 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 3.3 49.4 - - + -
118E GLN* 3.9 0.2 - - - +
97F CYS* 3.9 3.1 - - - -
124F LYS* 1.3 108.5 - - + +
126F GLN* 1.3 64.6 + - - +
127F ARG* 4.3 3.5 - - - +
128F VAL* 3.8 24.3 - - + +
152F VAL* 4.1 16.8 - - + -
154F HIS 3.3 11.0 - - - +
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Residues in contact with GLN 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LYS* 3.3 4.9 + - - +
125F PRO* 1.3 73.8 - - - +
127F ARG* 1.3 67.9 + - + +
128F VAL 4.4 0.2 + - - -
154F HIS* 2.9 40.9 + - - +
155F CYS 4.6 4.0 - - - +
156F ARG* 4.0 51.0 + - + +
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F PRO* 4.3 1.4 - - - +
126F GLN* 1.3 92.6 + - + +
128F VAL* 1.3 76.8 + - - +
129F THR* 4.1 18.5 - - + +
152F VAL* 4.0 2.4 - - - -
153F LYS* 3.2 34.6 + - + +
154F HIS* 3.7 10.1 + - - +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 4.4 12.6 - - + +
125F PRO* 3.8 32.8 - - + +
126F GLN 4.3 0.4 - - - -
127F ARG* 1.3 82.2 - - - +
129F THR* 1.3 69.4 + - - +
150F GLN* 3.7 42.4 - - + +
151F LYS 3.5 8.7 - - - +
152F VAL* 5.0 2.9 - - + -
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Residues in contact with THR 129 (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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127F ARG* 4.1 21.3 - - + +
128F VAL* 1.3 80.7 - - - +
130F SER* 1.3 64.2 + - - +
131F VAL* 4.5 3.5 - - - +
150F GLN* 3.4 4.8 - - - -
151F LYS* 2.7 55.8 + - - +
153F LYS* 3.8 25.4 - - + +
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Residues in contact with SER 130 (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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129F THR* 1.3 78.5 - - - +
131F VAL* 1.3 65.3 + - - +
148F LYS* 2.9 50.8 + - - +
149F ILE 3.4 6.4 + - - -
150F GLN* 4.8 4.2 - - - +
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Residues in contact with VAL 131 (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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92F ILE* 6.3 0.7 - - + -
129F THR* 4.5 4.9 - - - +
130F SER* 1.3 81.0 + - - +
132F ILE* 1.3 75.2 + - - +
133F VAL* 4.6 8.7 - - + -
147F LYS 3.3 2.3 - - - +
148F LYS* 3.7 2.4 - - - -
149F ILE* 2.9 38.7 + - + +
151F LYS* 3.6 39.5 - - + -
153F LYS* 5.7 1.8 - - - +
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Residues in contact with ILE 132 (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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130F SER 4.3 0.2 - - - -
131F VAL* 1.3 79.6 - - - +
133F VAL* 1.3 73.2 + - - +
134F GLU* 4.6 5.2 - - + +
146F ILE* 3.5 41.1 - - + -
147F LYS 3.6 1.6 - - - -
148F LYS* 4.1 30.1 - - + +
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Residues in contact with VAL 133 (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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82F VAL* 3.9 17.7 - - + -
90F ARG* 4.7 13.0 - - + +
92F ILE* 3.8 25.4 - - + -
131F VAL* 4.4 9.9 - - + +
132F ILE* 1.3 81.9 - - - +
134F GLU* 1.3 62.5 + - - +
135F LEU* 3.5 21.2 - - + +
145F ARG 3.7 1.4 - - - +
146F ILE 3.5 0.3 - - - -
147F LYS* 2.7 45.9 + - - +
149F ILE* 4.2 19.1 - - + -
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Residues in contact with GLU 134 (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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90F ARG* 3.9 18.7 - - - +
132F ILE* 4.3 8.4 - - + +
133F VAL* 1.3 74.2 - - - +
135F LEU* 1.3 66.9 + - - +
136F GLU* 3.3 21.6 - - - +
144F PHE* 3.0 43.1 - - + +
145F ARG 3.6 7.9 - - - +
146F ILE* 4.4 11.4 - - + +
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Residues in contact with LEU 135 (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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82F VAL* 3.4 32.1 - - + +
83F SER* 4.1 1.1 - - - -
84F GLU* 4.0 23.6 - - + +
87F CYS* 3.8 17.5 - - + -
88F ARG 3.2 21.8 - - - +
90F ARG* 5.0 6.5 - - + +
133F VAL* 3.5 37.2 - - + +
134F GLU* 1.3 76.0 - - - +
136F GLU* 1.3 65.3 + - - +
137F CYS* 3.4 12.0 + - - -
144F PHE* 3.5 6.9 - - - +
145F ARG* 3.4 23.1 + - + +
147F LYS* 4.3 7.0 - - + -
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Residues in contact with GLU 136 (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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87F CYS* 3.2 0.7 - - - -
88F ARG* 2.7 44.5 + - + +
134F GLU* 3.3 30.5 - - - +
135F LEU* 1.3 72.7 - - - +
137F CYS* 1.3 58.0 + - - +
138F PRO* 3.9 7.7 - - + +
143F PRO* 3.9 12.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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