Contacts of the strand formed by residues 117 - 136 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA* 3.9 32.3 - - + -
40B PRO* 4.1 2.9 - - + -
94B SER* 4.1 16.4 - - - -
96B LEU* 4.5 10.5 - - + -
106B TYR* 3.5 38.1 - + + +
104G PHE* 4.3 14.1 - - + -
105G TYR* 3.2 10.1 - - - -
106G ILE* 3.0 44.4 + - + +
116G SER* 1.3 75.9 - - - +
118G GLN* 1.3 59.2 + - - +
119G SER* 4.0 24.5 - - - -
161G ASN* 3.5 38.6 - - + -
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Residues in contact with GLN 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G SER* 3.9 0.4 + - - -
104G PHE 3.3 11.2 + - - -
105G TYR* 3.4 22.1 - - + -
116G SER* 4.3 1.0 + - - +
117G PHE* 1.3 75.2 - - - +
119G SER* 1.3 79.7 + - - +
120G CYS* 3.9 2.3 + - + +
161G ASN* 2.9 29.7 + - - +
162G LEU 4.2 6.1 + - - +
122H PHE* 3.6 19.4 - - + +
123H CYS 3.2 23.6 + - - -
124H LYS* 2.9 27.8 - - - +
125H PRO* 3.9 0.5 - - - +
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Residues in contact with SER 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.1 12.5 - - - +
40B PRO* 5.5 0.4 - - - -
102G ASN 4.5 1.2 + - - -
103G SER* 2.8 31.7 + - - -
104G PHE* 2.9 39.9 + - - -
117G PHE* 4.0 23.0 - - - -
118G GLN* 1.3 84.3 + - - +
120G CYS* 1.3 57.6 + - - +
159G SER* 4.7 9.2 - - - -
160G VAL 3.2 9.6 - - - -
122H PHE* 3.4 2.3 - - - +
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Residues in contact with CYS 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLN* 3.9 3.1 + - + +
119G SER* 1.3 73.8 - - - +
121G ALA* 1.3 59.5 + - - +
122G PHE* 3.6 6.6 - - - -
159G SER* 3.1 2.6 - - - -
160G VAL* 2.8 45.4 + - + +
162G LEU* 5.6 5.2 - - + -
120H CYS* 3.4 31.6 - - - -
121H ALA 3.8 3.6 - - - -
122H PHE* 3.5 28.7 - - + -
160H VAL* 5.3 2.9 - - - -
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Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CYS* 3.6 19.7 - - + +
102G ASN 3.3 26.9 - - - +
103G SER* 4.8 0.9 - - - -
119G SER 4.2 0.8 - - - -
120G CYS* 1.3 74.1 - - - +
122G PHE* 1.3 64.3 + - - +
157G CYS* 5.6 0.2 - - + -
158G MET 3.2 12.3 - - - +
159G SER* 3.8 7.9 - - - -
103H SER* 4.2 3.0 + - - -
120H CYS* 3.7 0.2 - - - -
121H ALA* 2.9 38.9 + - - +
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Residues in contact with PHE 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU* 3.8 20.9 - - - -
101G CYS* 4.0 5.0 - - - -
120G CYS* 3.6 18.4 - - - -
121G ALA* 1.3 80.8 - - - +
123G CYS* 1.3 63.0 + - - +
124G LYS* 3.3 36.6 + - + +
156G ARG 3.6 0.3 - - - +
158G MET* 3.0 33.2 + - + -
159G SER* 3.8 13.7 - - - -
160G VAL* 4.0 17.9 - - + -
103H SER* 3.4 6.5 - - - -
118H GLN* 3.7 12.6 - - + +
119H SER 3.6 17.3 - - - +
120H CYS* 4.1 20.6 - - + -
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Residues in contact with CYS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G CYS* 2.1 49.8 - - + -
97G CYS* 3.7 22.5 - - - +
98G TYR 3.5 7.6 - - - -
99G GLY* 3.5 32.8 - - - +
101G CYS* 3.8 8.0 - - - -
122G PHE* 1.3 69.2 - - - +
124G LYS* 1.3 58.8 + - - +
155G CYS* 4.0 1.3 - - - -
156G ARG 3.8 1.1 - - - -
103H SER* 3.2 14.6 + - - +
104H PHE 4.2 0.2 - - - -
105H TYR* 4.0 4.9 + - - +
118H GLN* 3.1 14.4 + - - -
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Residues in contact with LYS 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS* 6.1 0.6 + - - -
42B GLU* 4.9 8.3 + - - +
97G CYS* 3.7 6.5 - - - -
122G PHE* 3.6 31.5 - - + +
123G CYS* 1.3 73.4 - - - +
125G PRO* 1.4 89.5 - - + +
126G GLN* 3.3 0.4 + - - +
155G CYS* 3.3 0.5 - - - -
156G ARG* 2.9 39.5 + - + +
158G MET* 4.3 14.8 - - + +
105H TYR* 4.6 0.2 - - - -
118H GLN* 3.1 23.6 - - - +
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Residues in contact with PRO 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G CYS* 3.9 4.5 - - - -
124G LYS* 1.4 107.5 - - + +
126G GLN* 1.3 64.0 + - - +
127G ARG 4.3 11.9 - - - +
128G VAL* 4.8 8.5 + - + +
152G VAL* 4.1 20.4 - - + -
154G HIS 3.3 11.4 - - - +
105H TYR* 3.7 42.8 - - + -
118H GLN* 4.1 0.4 - - - +
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Residues in contact with GLN 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E GLN* 2.9 23.8 + - - +
127E ARG* 5.6 0.9 - - - -
154E HIS* 2.8 51.6 + - + +
124G LYS* 3.3 4.7 + - - +
125G PRO* 1.3 73.9 - - - +
127G ARG* 1.3 64.7 + - + +
128G VAL 4.4 0.2 + - - -
154G HIS* 2.9 27.2 + - - +
155G CYS 4.6 6.3 + - - -
156G ARG* 3.9 37.6 + - + +
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Residues in contact with ARG 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E GLN* 5.5 2.2 - - - +
127E ARG* 3.5 43.5 - - - +
125G PRO* 4.3 5.7 - - - +
126G GLN* 1.3 89.6 - - + +
128G VAL* 1.3 66.9 + - - +
129G THR* 2.6 35.5 - - + +
151G LYS 4.0 0.2 - - - +
152G VAL* 4.0 2.4 - - - -
153G LYS* 3.2 59.8 + - + +
154G HIS* 3.7 12.4 + - - +
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G PRO* 4.8 10.6 - - + +
126G GLN 4.3 0.8 + - - -
127G ARG* 1.3 76.8 - - - +
129G THR* 1.3 71.1 + - - +
150G GLN* 3.7 45.3 - - + +
151G LYS 3.4 11.4 - - - +
152G VAL* 4.9 3.8 - - + +
105H TYR* 6.0 1.1 - - - +
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Residues in contact with THR 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G ARG* 2.6 51.1 + - + +
128G VAL* 1.3 81.4 - - - +
130G SER* 1.3 63.8 + - - +
131G VAL* 4.5 4.8 - - - +
150G GLN* 3.4 4.8 - - - -
151G LYS* 2.7 55.8 + - - +
153G LYS* 3.8 13.4 - - + +
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Residues in contact with SER 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 5.1 2.9 - - - +
129G THR* 1.3 78.2 - - - +
131G VAL* 1.3 66.1 + - - +
148G LYS* 3.8 29.3 - - - +
149G ILE 3.4 7.7 + - - -
150G GLN* 4.8 3.4 - - - +
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Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET 3.7 7.6 - - - +
76C ASP* 3.5 33.7 - - - +
77C PRO* 3.7 15.7 - - + -
78C GLU* 4.7 2.7 - - - -
92G ILE* 6.1 0.9 - - + -
129G THR* 4.5 5.2 - - - +
130G SER* 1.3 81.1 + - - +
132G ILE* 1.3 75.4 + - - +
133G VAL* 3.6 4.4 + - + -
147G LYS 3.3 1.9 - - - +
148G LYS* 4.6 2.2 - - - -
149G ILE* 2.9 37.1 + - + +
151G LYS* 3.6 33.7 - - + -
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Residues in contact with ILE 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 3.7 8.8 - - - +
78C GLU* 3.1 50.6 + - + +
130G SER 4.3 0.4 - - - -
131G VAL* 1.3 80.7 - - - +
133G VAL* 1.3 75.6 + - - +
134G GLU* 4.6 6.1 - - + +
146G ILE* 4.8 28.0 - - + -
147G LYS 3.5 4.0 - - - +
148G LYS* 4.5 29.6 - - + -
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO* 4.0 14.4 - - + -
82G VAL* 3.8 16.8 - - + -
90G ARG* 4.7 8.5 - - + -
92G ILE* 3.8 34.3 - - + -
131G VAL* 4.4 5.2 - - + +
132G ILE* 1.3 80.8 - - - +
134G GLU* 1.3 62.9 + - - +
135G LEU* 3.5 21.6 - - + +
145G ARG 3.7 1.2 - - - +
146G ILE 3.5 0.3 - - - -
147G LYS* 2.7 44.7 + - - +
149G ILE* 4.2 17.3 - - + -
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Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 5.9 1.0 - - - +
90G ARG* 3.9 24.9 + - - +
132G ILE* 4.3 6.8 - - + +
133G VAL* 1.3 73.9 - - - +
135G LEU* 1.3 66.8 + - - +
144G PHE* 3.0 44.3 - - + +
145G ARG 3.6 7.4 - - - +
146G ILE* 4.4 11.2 - - + +
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G VAL* 3.4 32.3 - - + +
83G SER* 4.1 1.3 - - - -
84G GLU* 4.0 23.8 - - + +
87G CYS* 3.8 17.7 - - + -
88G ARG* 3.2 23.8 - - - +
90G ARG* 5.0 6.5 - - + +
133G VAL* 3.5 37.2 - - + +
134G GLU* 1.3 78.6 - - - +
136G GLU* 1.3 63.0 + - - +
137G CYS* 3.4 11.4 + - - -
144G PHE* 3.5 7.2 - - - +
145G ARG* 3.4 22.7 + - + +
147G LYS* 4.3 6.1 - - + -
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Residues in contact with GLU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 3.2 42.4 - - - +
87G CYS* 3.2 0.5 - - - -
88G ARG* 2.7 62.2 + - + +
135G LEU* 1.3 70.9 - - - +
137G CYS* 1.3 57.3 + - - +
138G PRO* 3.6 17.9 - - + +
143G PRO 4.6 5.8 - - - +
144G PHE* 5.7 0.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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