Contacts of the strand formed by residues 90 - 106 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 3.5 37.4 + - - +
54D PHE 5.7 0.2 - - - +
73D ASN* 2.8 38.0 + - - +
74D SER* 4.8 2.0 - - - +
77D PRO* 3.7 31.3 - - - +
82D PRO* 5.4 4.4 - - - +
81E THR* 3.8 2.0 - - - +
82E VAL* 2.9 35.7 + - - +
88E ARG* 3.6 18.9 + - - +
89E SER* 1.3 73.3 - - - +
91E THR* 1.3 63.9 + - - +
92E ILE* 4.2 14.9 - - + +
133E VAL* 4.7 11.7 - - + -
134E GLU 3.8 25.7 + - - +
135E LEU* 4.7 4.0 - - + +
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Residues in contact with THR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 5.1 2.1 + - - +
54D PHE* 3.4 54.9 + - + +
55D PRO* 4.7 7.9 - - + +
74D SER* 4.4 4.3 - - - -
79E ARG* 4.3 14.6 - - + -
80E GLN 3.4 10.3 - - - +
81E THR* 4.4 10.6 + - - +
89E SER 4.4 0.4 + - - -
90E ARG* 1.3 75.7 + - - +
92E ILE* 1.3 73.3 + - - +
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 4.8 0.4 - - - -
74D SER* 3.0 26.0 - - - +
75D MET 4.3 7.6 - - - +
77D PRO* 4.0 13.0 - - + -
79E ARG* 3.7 1.9 - - - -
80E GLN* 2.7 40.0 + - + +
82E VAL* 3.6 27.4 - - + -
90E ARG* 4.2 18.2 - - + +
91E THR* 1.3 87.5 - - - +
93E LEU* 1.3 69.9 + - - +
94E ASN* 3.8 5.8 - - + +
131E VAL* 6.1 0.9 - - + -
133E VAL* 3.8 28.3 - - + -
149E ILE* 5.3 7.2 - - + -
151E LYS* 5.1 4.5 - - + -
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.5 25.6 - - + -
71D LEU* 3.1 37.2 - - + -
74D SER* 3.0 21.9 + - - +
75D MET* 3.6 29.7 - - + +
77E PRO* 4.8 8.5 - - + -
78E LEU 3.7 12.3 - - - +
79E ARG* 3.8 20.0 - - + +
92E ILE* 1.3 78.3 - - - +
94E ASN* 1.3 67.0 + - - +
95E ARG* 5.5 0.3 - - - +
151E LYS* 3.7 8.7 + - - +
31G PRO* 4.3 17.5 - - + -
32G SER 5.3 0.9 - - - +
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Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E PRO* 4.0 2.9 - - - +
78E LEU* 2.9 32.9 + - + +
80E GLN* 2.7 32.9 + - + +
92E ILE* 3.8 3.4 + - + +
93E LEU* 1.3 79.3 - - - +
95E ARG* 1.3 85.7 + - - +
149E ILE* 4.0 5.3 - - - +
150E GLN 2.9 25.8 + - - -
151E LYS* 3.5 13.3 - - - +
152E VAL 3.2 22.7 + - - -
107F PRO* 4.1 16.4 - - + +
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Residues in contact with ARG 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS 4.7 1.8 + - - -
30B ASP* 2.1 40.6 + - - +
31B MET* 4.5 4.8 + - - +
32B GLY* 5.5 2.2 - - - +
75D MET* 4.2 11.9 - - - +
75E THR* 2.5 40.6 - - - +
76E GLN 3.1 13.7 - - - +
77E PRO* 5.0 1.3 - - + -
78E LEU* 4.1 6.3 - - - -
93E LEU 5.5 0.4 - - - +
94E ASN* 1.3 86.7 + - - +
96E PHE* 1.3 59.4 + - - +
151E LYS* 3.4 23.7 - - - +
152E VAL* 3.1 38.4 + - + +
153E LYS* 3.6 26.7 - - - +
107F PRO* 3.1 23.2 - - - +
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Residues in contact with PHE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E THR* 3.5 3.5 - - - -
76E GLN* 2.8 62.3 + - + +
77E PRO 3.5 17.9 - - - -
78E LEU* 4.1 10.3 - - + -
95E ARG* 1.3 74.1 - - - +
97E CYS* 1.3 73.0 + - - +
98E TYR* 3.8 22.4 - + + -
152E VAL* 5.0 0.7 - - - -
155E CYS* 4.5 0.7 - - - -
62F VAL* 3.5 41.7 - - + -
63F THR* 4.3 14.8 - - + -
104F PHE* 4.4 12.8 - + - -
105F TYR* 3.0 19.1 - - - +
106F ILE* 4.1 13.0 - - + -
107F PRO* 4.2 3.1 - - + -
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Residues in contact with CYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E LYS 3.6 0.4 - - - -
96E PHE* 1.3 78.6 - - - +
98E TYR* 1.3 61.0 + - - +
123E CYS* 3.6 20.4 - - - +
124E LYS 3.7 0.2 - - - -
125E PRO* 3.6 26.5 - - - -
152E VAL* 3.8 11.7 - - - -
155E CYS* 2.0 50.3 - - + -
104F PHE* 3.3 5.1 - - - -
105F TYR* 2.8 36.7 + - + +
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Residues in contact with TYR 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E TRP* 3.4 33.9 - + - -
74E LYS* 3.0 29.4 + - - +
76E GLN* 4.4 16.3 - - + +
96E PHE* 3.8 19.7 + + + -
97E CYS* 1.3 75.0 - - - +
99E GLY* 1.3 64.5 + - - +
123E CYS* 3.5 3.8 - - - -
67F TYR 4.2 18.2 - - - -
68F LEU* 3.8 10.5 - - + +
69F LYS* 3.1 24.2 + - + +
102F ASN* 2.5 36.0 + - + -
103F SER 3.3 10.8 - - - -
104F PHE* 3.2 35.2 - + + -
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Residues in contact with GLY 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E TRP* 3.2 22.2 - - - -
73E CYS* 3.7 5.2 - - - -
98E TYR* 1.3 77.6 - - - +
100E GLN* 1.3 63.4 + - - +
101E CYS* 4.0 1.8 - - - -
123E CYS* 3.4 12.8 - - - -
101F CYS 3.7 0.3 - - - +
102F ASN* 3.4 3.6 - - - -
103F SER* 2.9 33.6 + - - +
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Residues in contact with GLN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASP* 3.8 3.8 - - - -
72E TRP* 2.9 66.1 + - + +
99E GLY* 1.3 71.5 - - - +
101E CYS* 1.3 61.2 + - - +
69F LYS* 3.5 9.7 + - - +
70F SER 3.2 32.9 + - - +
71F ASP* 3.5 6.1 + - - +
72F TRP* 4.8 4.9 + - - -
100F GLN* 4.0 30.1 - - + +
101F CYS 3.3 7.0 - - - +
102F ASN* 2.9 34.0 + - - +
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Residues in contact with CYS 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASP* 3.6 2.5 - - - +
72E TRP 4.5 0.2 - - - -
99E GLY 4.6 0.9 - - - -
100E GLN* 1.3 76.4 - - - +
102E ASN* 1.3 64.4 + - - +
103E SER* 3.7 3.8 + - - -
121E ALA* 3.6 24.3 - - + +
122E PHE* 4.0 2.2 - - - +
123E CYS* 3.9 27.1 - - - -
157E CYS* 2.1 53.8 - - + -
100F GLN* 3.4 15.4 - - - -
101F CYS* 3.4 13.1 + - - +
103F SER* 5.2 2.2 - - - -
121F ALA 5.5 0.5 - - - +
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Residues in contact with ASN 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.4 8.5 - - + +
68E LEU* 5.3 4.9 - - - +
69E LYS 2.9 19.5 + - - -
70E SER* 4.8 0.2 - - - +
71E ASP* 2.8 32.9 + - - +
101E CYS* 1.3 76.6 - - - +
103E SER* 1.3 59.3 + - - +
104E PHE* 4.1 12.8 - - + -
119E SER* 4.5 1.7 + - - -
121E ALA* 3.3 17.7 - - - +
159E SER* 5.1 2.4 - - - -
98F TYR* 2.6 36.2 + - + -
99F GLY 3.3 4.5 - - - -
100F GLN* 3.2 15.1 + - - +
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Residues in contact with SER 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E CYS 4.3 4.0 - - - -
102E ASN* 1.3 78.2 - - - +
104E PHE* 1.3 64.4 + - - +
118E GLN* 3.9 0.9 + - - -
119E SER* 2.8 32.4 + - - -
121E ALA* 4.8 0.9 - - - -
98F TYR* 3.5 6.4 - - - -
99F GLY 3.0 32.4 + - - -
101F CYS* 5.1 1.8 - - - -
121F ALA 4.4 6.1 - - - -
122F PHE* 3.2 8.5 - - - -
123F CYS* 3.0 30.5 + - - +
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Residues in contact with PHE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.5 27.4 - - + -
39A ALA* 4.6 4.7 - - + -
96A LEU* 3.6 22.7 - - + -
104A VAL* 5.3 2.2 - - + -
62E VAL* 5.6 2.5 - - + -
63E THR* 5.8 0.4 - - + -
68E LEU* 3.5 28.0 - - + -
102E ASN* 4.1 16.8 - - + -
103E SER* 1.3 76.0 + - - +
105E TYR* 1.3 59.0 + - - +
106E ILE* 4.0 17.3 - - + -
117E PHE* 3.7 3.8 - - + +
118E GLN* 3.3 7.8 + - - -
119E SER* 2.9 39.6 + - - +
96F PHE* 4.3 14.8 - + - -
97F CYS 3.2 12.1 - - - +
98F TYR* 3.3 34.5 - + + -
123F CYS 3.9 4.9 - - - -
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Residues in contact with TYR 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 1.3 74.8 - - - +
106E ILE* 1.3 60.9 + - - +
107E PRO* 3.9 15.4 - - + +
116E SER* 3.6 34.8 + - - -
117E PHE 3.2 13.2 - - - -
118E GLN* 3.4 26.5 - - + +
96F PHE* 3.3 8.0 - - - +
97F CYS* 2.8 45.0 + - + +
123F CYS 4.0 1.8 - - - +
125F PRO* 3.3 40.8 - - + -
128F VAL* 4.4 9.8 - - + +
150F GLN* 4.2 12.0 + - - +
152F VAL* 3.5 24.9 - - + -
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Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.3 16.8 - - + -
106A TYR* 4.5 13.9 - - + -
60E LEU* 4.1 23.8 - - + -
62E VAL* 4.6 14.6 - - + -
104E PHE* 4.0 13.7 - - + -
105E TYR* 1.3 79.5 - - - +
107E PRO* 1.3 83.4 - - + +
110E VAL* 4.4 4.3 - - + -
116E SER* 3.4 3.6 - - - -
117E PHE* 3.0 66.2 + - + -
78F LEU* 4.4 3.8 - - + -
96F PHE* 4.3 11.4 - - + -
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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
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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