Contacts of the strand formed by residues 117 - 133 (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 PHE 117 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H PHE* 4.1 17.7 - + + -
105H TYR* 3.2 10.4 - - - -
106H ILE* 3.0 54.0 + - + +
115H ASP 5.3 0.7 - - - +
116H SER* 1.3 75.6 - - - +
118H GLN* 1.3 60.5 + - - +
119H SER* 3.7 31.9 - - - -
161H ASN* 3.5 34.5 - - + +
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Residues in contact with GLN 118 (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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122G PHE* 3.7 14.5 - - + +
123G CYS 3.1 23.4 + - - -
124G LYS* 3.1 25.4 - - - +
125G PRO* 4.1 0.3 - - - +
103H SER* 3.9 0.6 + - - -
104H PHE 3.3 17.7 + - - -
105H TYR* 3.3 23.1 - - + -
116H SER* 4.3 1.3 + - - +
117H PHE* 1.3 75.8 - - - +
119H SER* 1.3 74.9 + - - +
120H CYS* 3.9 14.1 + - - -
160H VAL 3.8 0.3 - - - +
161H ASN* 3.2 27.0 + - - +
162H LEU* 3.7 13.7 + - + +
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G PHE* 3.6 1.2 - - - +
102H ASN 4.5 1.6 + - - -
103H SER* 2.8 28.5 + - - -
104H PHE* 2.9 41.6 + - - -
117H PHE* 3.7 22.9 - - - -
118H GLN* 1.3 82.5 + - - +
120H CYS* 1.3 60.0 + - - +
159H SER* 4.7 13.0 - - - -
160H VAL 3.2 11.0 - - - -
161H ASN* 4.6 0.2 - - - +
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Residues in contact with CYS 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G CYS* 3.4 25.8 - - - -
121G ALA 3.7 4.5 - - - -
122G PHE* 4.1 17.7 - - + -
118H GLN* 4.0 20.4 - - - -
119H SER* 1.3 79.6 - - - +
121H ALA* 1.3 59.9 + - - +
122H PHE* 3.8 5.0 - - - -
159H SER* 3.1 2.8 - - - -
160H VAL* 2.8 40.0 + - + +
162H LEU* 4.2 26.2 - - - -
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CYS 5.5 0.7 - - - +
103G SER* 4.1 3.2 + - - -
121G ALA* 2.9 37.7 + - - +
101H CYS* 3.6 20.2 - - + +
102H ASN 3.3 26.7 - - - +
103H SER* 4.8 2.0 + - - -
119H SER 4.2 0.4 + - - -
120H CYS* 1.3 74.3 - - - +
122H PHE* 1.3 63.8 + - - +
158H MET 3.2 13.5 - - - +
159H SER* 3.8 7.4 - - - -
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Residues in contact with PHE 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G SER* 3.1 6.5 - - - +
118G GLN* 3.6 12.3 - - + +
119G SER 3.4 20.0 - - - +
120G CYS* 3.5 28.9 - - + -
101H CYS* 4.0 5.5 - - - -
120H CYS 3.8 13.0 - - - -
121H ALA* 1.3 76.6 - - - +
123H CYS* 1.3 61.8 + - - +
124H LYS* 3.4 26.4 + - + -
156H ARG 3.6 0.2 - - - +
158H MET* 3.0 46.9 + - + -
159H SER* 4.2 2.7 - - - -
160H VAL* 4.0 27.1 - - + -
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Residues in contact with CYS 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G SER* 3.0 14.5 + - - +
104G PHE 3.9 1.7 - - - -
105G TYR 3.9 6.6 + - - -
118G GLN* 3.2 11.8 + - - -
73H CYS* 2.0 50.5 - - + -
97H CYS* 3.6 22.9 - - - +
98H TYR 3.5 8.1 - - - -
99H GLY* 3.5 32.3 - - - +
101H CYS* 3.8 8.0 - - - -
122H PHE* 1.3 69.1 - - - +
124H LYS* 1.3 57.6 + - - +
155H CYS* 4.0 0.9 - - - -
156H ARG 3.8 1.6 - - - -
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Residues in contact with LYS 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G TYR* 4.3 0.2 - - - -
118G GLN* 2.9 27.6 - - - +
97H CYS* 3.7 5.6 - - - -
122H PHE* 3.7 30.9 - - + +
123H CYS* 1.3 73.7 - - - +
125H PRO* 1.3 88.7 - - + +
126H GLN* 3.3 0.8 + - - +
155H CYS* 3.3 0.7 - - - -
156H ARG* 2.9 37.7 + - + +
158H MET* 4.3 13.4 - - + +
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Residues in contact with PRO 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G TYR* 3.3 49.6 - - + -
118G GLN* 3.9 0.2 - - - +
97H CYS* 3.9 3.4 - - - -
124H LYS* 1.3 106.0 - - + +
126H GLN* 1.3 64.7 + - - +
127H ARG 4.3 3.3 - - - +
128H VAL* 3.8 24.3 - - + +
152H VAL* 4.1 16.8 - - + -
154H HIS 3.3 12.1 - - - +
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Residues in contact with GLN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LYS* 3.3 4.4 + - - +
125H PRO* 1.3 74.8 - - - +
127H ARG* 1.3 68.2 + - + +
128H VAL 4.4 0.3 + - - -
154H HIS* 2.9 39.9 + - - +
155H CYS 4.7 3.5 - - - +
156H ARG* 3.9 48.8 + - + +
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Residues in contact with ARG 127 (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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125H PRO* 4.3 1.6 - - - +
126H GLN* 1.3 95.1 + - + +
128H VAL* 1.3 76.2 + - - +
129H THR* 4.1 19.2 - - + +
151H LYS 4.0 0.3 - - - +
152H VAL* 4.0 2.4 - - - -
153H LYS* 3.2 34.6 + - + +
154H HIS* 3.7 9.3 + - - +
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G TYR* 4.4 12.8 - - + +
125H PRO* 3.8 32.1 - - + +
126H GLN 4.3 0.8 + - - -
127H ARG* 1.3 81.4 - - - +
129H THR* 1.3 69.8 + - - +
150H GLN* 3.7 42.8 - - + +
151H LYS 3.5 8.3 - - - +
152H VAL* 5.0 3.1 - - + -
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Residues in contact with THR 129 (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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127H ARG* 4.1 21.5 - - + +
128H VAL* 1.3 80.2 - - - +
130H SER* 1.3 63.9 + - - +
131H VAL* 4.5 3.7 - - - +
150H GLN* 3.4 5.0 - - - -
151H LYS* 2.7 56.3 + - - +
153H LYS* 3.8 25.5 - - + +
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Residues in contact with SER 130 (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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129H THR* 1.3 77.8 - - - +
131H VAL* 1.3 65.8 + - - +
148H LYS* 3.3 42.6 + - - +
149H ILE 3.4 7.8 + - - -
150H GLN* 4.8 3.4 - - - +
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Residues in contact with VAL 131 (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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92H ILE* 6.2 0.9 - - + -
129H THR* 4.5 4.9 - - - +
130H SER* 1.3 81.4 + - - +
132H ILE* 1.3 75.3 + - - +
133H VAL* 4.6 8.5 - - + -
147H LYS 3.3 2.1 - - - +
148H LYS* 3.7 2.4 - - - -
149H ILE* 2.9 38.0 + - + +
151H LYS* 3.7 39.3 - - + -
153H LYS* 5.7 1.8 - - - +
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Residues in contact with ILE 132 (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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130H SER 4.3 0.2 - - - -
131H VAL* 1.3 80.0 - - - +
133H VAL* 1.3 75.5 + - - +
134H GLU* 4.6 6.1 - - + +
146H ILE* 4.8 29.8 - - + -
147H LYS 3.6 4.7 - - - +
148H LYS* 4.6 28.0 - - + +
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Residues in contact with VAL 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H VAL* 3.9 28.0 - - + -
90H ARG* 4.7 14.6 - - + -
92H ILE* 3.8 26.7 - - + -
131H VAL* 4.4 9.9 - - + +
132H ILE* 1.3 80.1 - - - +
134H GLU* 1.3 66.8 + - - +
145H ARG 3.7 1.4 - - - +
146H ILE 3.5 0.7 - - - -
147H LYS* 2.7 45.1 + - - +
149H ILE* 4.2 18.6 - - + -
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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