Contacts of the strand formed by residues 90 - 106 (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 ARG 90 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU* 3.6 37.7 + - - +
54C PHE* 5.7 0.6 - - - +
73C ASN* 2.8 35.8 + - - +
74C SER* 4.8 2.4 - - - +
77C PRO* 3.8 31.7 - - - +
82C PRO* 5.5 3.8 - - - +
81G THR* 3.8 1.4 - - - -
82G VAL* 2.9 35.5 + - - +
88G ARG* 3.6 20.0 + - - +
89G SER* 1.3 75.4 - - - +
91G THR* 1.3 64.1 + - - +
92G ILE* 3.8 17.1 + - + +
133G VAL* 4.7 11.7 - - + -
134G GLU 3.9 25.1 + - - +
135G LEU* 5.2 3.4 - - + -
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Residues in contact with THR 91 (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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53C GLU* 5.1 2.3 + - - +
54C PHE* 3.6 55.5 + - + +
55C PRO* 4.7 8.2 - - + +
74C SER* 4.5 1.9 - - - -
79G ARG* 4.4 14.8 - - + -
80G GLN 3.4 10.1 - - - +
81G THR* 4.5 10.5 + - - +
89G SER 4.3 0.2 - - - -
90G ARG* 1.3 76.1 + - - +
92G ILE* 1.3 73.2 + - - +
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Residues in contact with ILE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 4.8 0.4 - - - -
74C SER* 3.0 22.2 - - - +
75C MET 4.5 7.4 - - - +
77C PRO* 4.1 11.4 - - + -
79G ARG* 3.7 1.9 - - - -
80G GLN* 2.7 40.7 + - + +
82G VAL* 3.6 27.6 - - + -
90G ARG* 4.2 18.6 - - + +
91G THR* 1.3 87.7 - - - +
93G LEU* 1.3 74.1 + - - +
94G ASN* 3.8 6.1 - - + +
131G VAL* 6.1 1.1 - - + -
133G VAL* 3.8 27.6 - - + -
149G ILE* 5.3 7.6 - - + -
151G LYS* 5.1 4.3 - - + -
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Residues in contact with LEU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 3.5 27.4 - - + -
71C LEU* 3.2 36.1 - - + -
74C SER* 3.2 20.8 + - - +
75C MET* 3.7 18.9 - - + +
31E PRO* 4.3 18.2 - - + -
32E SER 5.3 0.2 - - - +
77G PRO* 4.8 8.5 - - + -
78G LEU 3.8 12.3 - - - +
79G ARG* 3.8 20.9 - - + +
92G ILE* 1.3 78.9 - - - +
94G ASN* 1.3 66.2 + - - +
95G ARG* 5.5 0.2 - - - +
151G LYS* 3.7 18.5 + - - +
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Residues in contact with ASN 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PRO* 4.0 2.6 - - - +
78G LEU* 2.8 37.0 + - + +
80G GLN* 2.6 32.9 + - + +
92G ILE* 3.8 3.6 + - + +
93G LEU* 1.3 79.1 - - - +
95G ARG* 1.3 84.7 + - - +
149G ILE* 4.0 4.8 - - - +
150G GLN 2.9 25.7 + - - -
151G LYS* 3.5 13.4 - - + +
152G VAL 3.3 22.5 + - - +
107H PRO* 4.1 13.5 - - - +
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Residues in contact with ARG 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS 4.8 1.8 + - - -
30A ASP* 2.1 38.4 + - - +
31A MET* 4.5 4.6 + - - +
32A GLY* 5.5 2.2 - - - +
75C MET* 4.2 11.5 - - - -
75G THR* 2.5 41.4 - - - +
76G GLN 3.1 14.8 - - - +
77G PRO* 5.0 1.1 - - + -
78G LEU* 4.1 6.1 - - - -
93G LEU 5.5 0.2 - - - +
94G ASN* 1.3 87.7 + - - +
96G PHE* 1.3 59.6 + - - +
151G LYS* 3.4 24.6 - - - +
152G VAL* 3.1 37.7 + - + +
153G LYS* 3.6 27.5 - - - +
107H PRO* 3.1 22.9 - - - +
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Residues in contact with PHE 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G THR* 3.5 3.5 - - - -
76G GLN* 2.9 61.7 + - + -
77G PRO* 3.5 18.6 - - + -
78G LEU* 4.1 11.7 - - + -
95G ARG* 1.3 74.1 - - - +
97G CYS* 1.3 71.5 + - - +
98G TYR* 3.8 22.4 - + + -
155G CYS* 4.5 0.9 - - - -
62H VAL* 3.5 39.5 - - + -
63H THR* 4.2 17.9 - - + -
104H PHE* 4.4 12.1 - + - -
105H TYR* 3.0 19.1 - - - +
106H ILE* 4.1 12.6 - - + -
107H PRO* 4.2 3.4 - - + -
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Residues in contact with CYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LYS 3.6 0.4 - - - -
96G PHE* 1.3 77.4 - - - +
98G TYR* 1.3 61.0 + - - +
123G CYS* 3.7 20.2 - - - +
125G PRO* 3.6 26.7 - - - -
152G VAL* 3.8 12.1 - - - -
155G CYS* 2.0 50.3 - - + -
104H PHE* 3.3 5.1 - - - -
105H TYR* 2.8 39.0 + - + +
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Residues in contact with TYR 98 (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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72G TRP* 3.4 34.1 - + - -
74G LYS* 3.0 32.4 + - + +
76G GLN* 4.4 14.4 - - + -
96G PHE* 3.8 20.5 + + + -
97G CYS* 1.3 76.2 - - - +
99G GLY* 1.3 68.7 + - - +
123G CYS* 3.5 4.3 - - - -
67H TYR 4.1 19.5 - - - -
68H LEU* 3.7 11.8 - - + +
69H LYS* 3.1 23.2 + - + -
102H ASN* 2.6 34.8 + - + -
103H SER 3.4 7.4 - - - -
104H PHE* 3.2 34.1 - + + -
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Residues in contact with GLY 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G TRP* 3.2 22.9 - - - -
73G CYS* 3.7 5.2 - - - -
98G TYR* 1.3 77.7 - - - +
100G GLN* 1.3 63.3 - - - +
101G CYS* 4.0 1.3 - - - -
123G CYS* 3.5 12.0 - - - -
101H CYS 3.8 0.2 - - - +
102H ASN* 3.4 3.3 - - - -
103H SER* 2.9 34.0 + - - +
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Residues in contact with GLN 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LYS* 6.1 0.2 - - - -
71G ASP* 3.8 4.2 - - - -
72G TRP* 2.9 65.6 + - + +
99G GLY* 1.3 71.3 - - - +
101G CYS* 1.3 60.6 + - - +
69H LYS* 3.5 10.0 + - - +
70H SER 3.3 32.7 + - - +
71H ASP* 3.5 6.5 + - - +
72H TRP* 4.8 4.9 + - - -
100H GLN* 4.0 29.5 - - + +
101H CYS 3.3 7.0 - - - +
102H ASN* 2.9 34.3 + - - +
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Residues in contact with CYS 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ASP* 3.6 2.5 - - - +
99G GLY 4.6 0.7 - - - -
100G GLN* 1.3 75.8 - - - +
102G ASN* 1.3 65.2 + - - +
103G SER* 3.7 3.8 + - - -
121G ALA* 3.6 23.5 - - + +
122G PHE* 4.0 3.1 - - - +
123G CYS* 3.8 27.4 - - - -
157G CYS* 2.1 55.2 - - + -
100H GLN* 3.5 3.3 - - - -
101H CYS* 3.4 25.9 + - - +
103H SER* 5.1 2.0 - - - -
121H ALA 5.5 0.7 - - - +
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Residues in contact with ASN 102 (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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38B ILE* 5.5 6.8 - - + +
68G LEU* 5.3 5.5 - - - +
69G LYS 2.9 19.6 + - - -
71G ASP* 2.8 31.8 + - - +
101G CYS* 1.3 76.8 - - - +
103G SER* 1.3 58.8 + - - +
104G PHE* 4.1 13.9 - - + -
119G SER* 4.5 2.1 + - - -
121G ALA* 3.3 18.7 - - - +
159G SER* 5.1 2.1 - - - -
98H TYR* 2.6 37.5 + - + -
99H GLY 3.3 3.6 - - - -
100H GLN* 3.2 15.5 + - - +
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Residues in contact with SER 103 (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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101G CYS 4.3 4.5 - - - -
102G ASN* 1.3 77.9 - - - +
104G PHE* 1.3 64.3 + - - +
118G GLN* 3.9 0.7 + - - -
119G SER* 2.8 32.1 + - - -
121G ALA* 4.8 1.1 - - - -
98H TYR* 3.5 6.1 - - - -
99H GLY 3.0 32.8 + - - -
101H CYS* 5.1 1.8 - - - -
121H ALA 4.3 5.4 - - - -
122H PHE* 3.1 7.8 - - - +
123H CYS* 3.0 31.6 + - - +
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Residues in contact with PHE 104 (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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38B ILE* 3.5 27.6 - - + -
39B ALA* 4.6 4.5 - - + -
96B LEU* 3.6 26.9 - - + -
104B VAL* 5.4 2.5 - - + -
62G VAL* 5.6 2.7 - - + -
63G THR* 5.8 0.2 - - + -
68G LEU* 3.5 27.6 - - + -
102G ASN* 4.1 17.3 - - + -
103G SER* 1.3 77.5 + - - +
105G TYR* 1.3 62.3 + - - +
106G ILE* 5.1 4.0 - - + -
117G PHE* 3.7 10.3 - - + +
118G GLN* 3.3 7.4 + - - -
119G SER* 2.9 40.0 + - - +
96H PHE* 4.3 14.1 - + - -
97H CYS 3.2 12.1 - - - +
98H TYR* 3.2 36.6 - + + -
123H CYS 3.9 5.2 - - - -
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Residues in contact with TYR 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PHE* 1.3 74.8 - - - +
106G ILE* 1.3 62.3 + - - +
107G PRO* 3.8 15.3 - - + +
116G SER* 3.6 34.5 + - - -
117G PHE 3.2 13.2 - - - -
118G GLN* 3.4 26.5 - - + +
96H PHE* 3.3 7.1 - - - +
97H CYS* 2.8 43.3 + - + -
123H CYS 3.9 3.0 + - - +
125H PRO* 3.3 40.0 - - + +
128H VAL* 4.4 9.2 - - + +
150H GLN* 4.2 12.1 + - - +
152H VAL* 3.6 24.5 - - + -
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Residues in contact with ILE 106 (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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96B LEU* 3.7 33.0 - - + -
106B TYR* 3.9 23.6 - - + -
60G LEU* 4.0 21.5 - - + -
62G VAL* 3.7 19.5 - - + -
104G PHE* 5.1 3.4 - - + -
105G TYR* 1.3 80.6 - - - +
107G PRO* 1.3 83.1 - - + +
110G VAL* 4.4 2.5 - - + -
116G SER* 3.4 3.6 - - - -
117G PHE* 3.0 42.4 + - + -
78H LEU* 4.3 5.2 - - + -
96H PHE* 4.2 13.2 - - + -
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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) + - + + + + + -
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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