Contacts of the strand formed by residues 147 - 161 (chain H) 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 LYS 147 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G LYS* 5.4 6.1 - - - +
82H VAL* 3.6 30.3 - - + -
83H SER 2.9 29.8 + - - +
84H GLU* 3.0 30.9 + - + +
131H VAL 3.3 3.8 - - - +
132H ILE* 3.6 3.5 - - - -
133H VAL* 2.7 46.1 + - + +
145H ARG* 4.4 10.3 - - + +
146H ILE* 1.3 84.4 - - - +
148H LYS* 1.3 61.8 + - - +
149H ILE* 3.7 9.8 + - + -
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Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ARG* 5.2 12.8 + - - +
109G HIS* 5.3 4.2 + - - +
130H SER* 3.3 29.3 + - - +
131H VAL 3.7 5.1 - - - -
132H ILE* 4.6 20.5 - - + +
146H ILE* 5.6 6.1 - - + -
147H LYS* 1.3 72.4 - - - +
149H ILE* 1.3 67.2 + - - +
150H GLN 4.3 0.5 + - - -
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Residues in contact with ILE 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ARG 5.6 0.4 - - - +
109G HIS* 4.9 14.4 - - + +
80H GLN* 3.5 28.3 - - - +
82H VAL* 4.1 34.1 - - + -
92H ILE* 4.7 7.0 - - + -
94H ASN* 4.0 6.3 - - - +
129H THR 3.5 0.3 - - - +
130H SER* 3.4 5.5 - - - -
131H VAL* 2.9 39.6 + - + +
133H VAL* 4.2 18.6 - - + -
147H LYS* 4.3 12.1 - - + +
148H LYS* 1.3 83.2 - - - +
150H GLN* 1.3 77.3 + - - +
151H LYS* 3.6 5.7 + - + +
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Residues in contact with GLN 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G TYR* 4.2 13.8 + - - +
107G PRO* 4.1 12.2 - - + +
108G ARG* 2.9 64.4 + - + +
109G HIS* 6.2 1.6 - - - +
116G SER* 5.4 0.7 - - - -
94H ASN* 2.9 21.7 + - - -
128H VAL* 3.7 23.5 - - + +
129H THR 3.4 5.2 - - - +
130H SER* 4.8 3.8 - - - +
148H LYS 4.2 0.8 + - - -
149H ILE* 1.3 75.2 - - - +
151H LYS* 1.3 58.0 + - - +
152H VAL* 4.3 0.4 - - - -
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Residues in contact with LYS 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ILE* 6.0 2.9 - - + -
93H LEU 3.6 20.9 + - - +
94H ASN* 3.5 23.5 - - - +
95H ARG* 3.9 17.8 - - - +
128H VAL* 3.5 5.9 - - - +
129H THR* 2.7 50.6 + - - +
131H VAL* 3.7 31.2 - - + -
149H ILE* 4.4 5.6 - - + +
150H GLN* 1.3 77.0 - - - +
152H VAL* 1.3 65.0 + - - +
153H LYS* 3.4 33.9 + - - +
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Residues in contact with VAL 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G TYR* 3.6 33.9 - - + -
107G PRO* 3.6 17.7 - - + -
75H THR* 4.3 6.7 - - - +
94H ASN* 3.3 6.8 + - - +
95H ARG* 3.6 37.1 + - + +
96H PHE* 5.3 0.2 - - - -
97H CYS* 3.8 6.3 - - - -
125H PRO* 4.1 11.4 - - + -
127H ARG 4.0 3.8 - - - -
128H VAL* 4.8 4.3 - - + +
151H LYS* 1.3 72.5 + - - +
153H LYS* 1.3 66.6 + - - +
154H HIS 4.2 4.3 - - - +
155H CYS* 3.8 29.4 - - - -
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Residues in contact with LYS 153 (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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75H THR* 4.0 17.5 + - - +
95H ARG* 4.5 9.4 - - - +
127H ARG* 3.2 16.4 + - + +
129H THR* 3.8 36.1 - - + +
131H VAL* 5.8 1.1 - - - -
151H LYS* 3.4 32.3 - - - +
152H VAL* 1.3 80.9 - - - +
154H HIS* 1.3 87.9 + - + +
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Residues in contact with HIS 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H THR* 5.1 4.7 - - + -
125H PRO* 3.3 8.5 - - - +
126H GLN* 2.9 55.0 + - + +
127H ARG* 3.7 9.4 + - - +
152H VAL* 4.2 0.5 - - - +
153H LYS* 1.3 96.8 + - + +
155H CYS* 1.3 67.4 + - - +
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Residues in contact with CYS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H CYS* 3.4 29.5 + - - +
74H LYS 3.9 11.2 - - - +
75H THR* 4.0 12.7 - - - +
97H CYS* 2.0 55.0 - - + -
123H CYS* 4.0 0.4 - - - -
124H LYS 3.3 5.6 - - - +
126H GLN* 4.1 5.1 - - - +
152H VAL* 3.8 9.9 - - - -
154H HIS* 1.3 78.7 - - - +
156H ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 156 (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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73H CYS* 3.3 12.3 - - - -
122H PHE 3.6 0.2 - - - +
124H LYS* 2.9 31.5 + - + +
126H GLN* 3.9 43.8 + - + +
155H CYS* 1.3 77.9 - - - +
157H CYS* 1.3 63.4 + - - +
158H MET* 3.3 38.1 + - + +
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Residues in contact with CYS 157 (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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71H ASP* 3.3 33.0 - - + +
72H TRP 3.8 2.9 - - - -
73H CYS* 3.6 18.4 - - - +
101H CYS* 2.0 51.8 - - + -
122H PHE 3.6 4.9 - - - -
156H ARG* 1.3 72.6 - - - +
158H MET* 1.3 80.7 + - - +
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Residues in contact with MET 158 (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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121H ALA* 3.2 4.4 - - - +
122H PHE* 3.0 52.2 + - + +
124H LYS* 4.3 15.7 - - + +
156H ARG* 3.3 50.7 - - - +
157H CYS* 1.3 89.5 - - - +
159H SER* 1.3 67.1 + - - +
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Residues in contact with SER 159 (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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102H ASN 5.1 2.0 - - - -
119H SER* 4.7 11.7 - - - -
120H CYS 3.1 15.5 - - - -
121H ALA* 3.8 11.9 - - - -
122H PHE* 4.2 3.3 - - - -
158H MET* 1.3 80.2 - - - +
160H VAL* 1.3 70.8 + - - +
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Residues in contact with VAL 160 (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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120G CYS* 5.3 2.0 - - - -
118H GLN 3.8 0.2 - - - +
119H SER* 3.2 6.5 - - - -
120H CYS* 2.8 48.8 + - + +
122H PHE* 4.0 23.6 - - + -
159H SER* 1.3 78.2 - - - +
161H ASN* 1.3 65.1 + - - +
162H LEU* 4.9 10.3 - - + -
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Residues in contact with ASN 161 (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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116H SER 5.0 0.6 + - - -
117H PHE* 3.5 38.3 - - + +
118H GLN 3.2 27.6 + - - +
160H VAL* 1.3 80.2 - - - +
162H LEU* 1.3 77.5 + - - +
163H SER* 4.1 4.3 + - - -
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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
------------------------------------------------------------
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