Contacts of the strand formed by residues 103 - 119 (chain A) 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 ASN 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE 3.5 0.5 - - - +
98A ILE* 3.4 2.9 - - - -
99A ASP* 3.0 43.5 + - - +
101A ALA* 4.1 17.1 - - - +
102A ASN* 1.3 77.9 - - - +
104A VAL* 1.3 63.2 + - - +
105A VAL* 3.6 13.8 + - + +
61E VAL* 4.2 21.6 - - + +
63E THR 3.6 7.6 - - - +
64E GLU* 3.7 21.4 - - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.7 7.9 - - + -
96A LEU* 3.9 31.6 - - + -
97A PHE 3.4 7.4 - - - +
98A ILE* 4.7 4.9 - - + +
102A ASN 3.8 0.2 + - - -
103A ASN* 1.3 70.8 - - - +
105A VAL* 1.3 65.3 + - - +
61E VAL* 4.0 1.0 - - - +
62E VAL* 3.1 27.9 + - + -
63E THR* 2.7 40.4 + - + +
64E GLU 3.9 0.2 - - - -
65E ARG* 3.9 17.5 - - + +
68E LEU* 3.8 32.3 - - + -
104E PHE* 5.3 1.1 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.3 7.3 - - - -
97A PHE* 2.7 67.1 + - + +
99A ASP* 3.9 15.3 - - + +
103A ASN* 3.7 23.1 - - + +
104A VAL* 1.3 81.8 - - - +
106A TYR* 1.3 64.6 + - - +
107A LYS* 4.7 0.2 - - + -
59E ALA* 3.4 31.9 - - + -
60E LEU 3.6 7.6 - - - +
61E VAL* 4.5 11.7 - - + -
62E VAL 4.6 0.2 - - - +
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.4 33.9 + - - -
95A ILE 3.5 11.4 - - - -
96A LEU* 3.7 20.0 - - + -
105A VAL* 1.3 73.6 - - - +
107A LYS* 1.3 59.1 + - - +
58E GLU 4.3 1.9 - - - +
59E ALA* 3.9 0.3 - - - -
60E LEU* 2.9 48.3 + - + +
62E VAL* 3.8 13.9 - - + +
106E ILE* 4.5 13.7 - - + -
110E VAL* 5.1 2.7 - - + -
111E LYS* 3.2 36.8 + - + -
115E ASP* 4.2 13.3 + - - +
116E SER 4.8 0.5 + - - -
117E PHE* 3.5 43.1 - + + +
161E ASN* 5.7 0.2 + - - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.4 2.2 - - - -
95A ILE 2.9 32.3 + - - +
97A PHE* 3.8 23.7 - - + -
105A VAL* 4.1 0.6 - - + -
106A TYR* 1.3 75.8 - - - +
108A GLN* 1.3 68.8 + - - +
109A TYR* 3.7 23.2 + - + -
50E LYS* 6.1 3.0 - - - +
55E SER* 3.9 32.0 + - - +
57E GLN* 3.7 24.2 + - + +
58E GLU 4.3 8.1 - - - +
59E ALA* 3.8 21.5 - - - -
111E LYS* 4.2 5.4 - - - +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 3.7 23.5 - - + +
93A ILE 3.6 8.7 - - - +
94A SER* 3.6 17.6 + - - +
107A LYS* 1.3 76.5 - - - +
109A TYR* 1.3 56.7 + - - +
110A GLU* 2.7 24.3 + - - +
55E SER* 2.7 29.8 + - - -
57E GLN* 3.0 38.5 - - + +
58E GLU 5.3 0.4 + - - -
111E LYS* 3.7 16.4 + - - +
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 3.1 21.8 - - - +
93A ILE 2.8 14.4 + - - +
95A ILE* 3.8 23.3 - - + -
97A PHE* 3.5 31.1 - + - -
107A LYS* 3.7 32.1 + - + +
108A GLN* 1.3 73.2 - - - +
110A GLU* 1.3 63.6 + - - +
112A MET* 3.6 21.0 - - + +
64C ASN* 4.0 3.4 - - - +
49E ILE* 3.4 27.5 + - + +
50E LYS* 4.9 2.1 + - - -
53E LEU* 3.4 41.7 - - + -
54E ALA 3.6 13.5 - - - -
55E SER* 3.7 12.6 - - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 3.3 23.0 - - - +
108A GLN* 2.7 32.8 + - - -
109A TYR* 1.3 76.6 - - - +
111A ASP* 1.3 77.8 + - - +
112A MET* 3.3 2.0 + - - +
64C ASN* 2.6 32.4 + - - +
54E ALA 4.4 4.1 + - - +
55E SER* 4.7 9.6 + - - +
56E SER 6.2 0.7 - - - +
57E GLN* 5.0 9.9 - - + -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.8 33.6 - - + +
91A SER 3.9 7.5 + - - -
110A GLU* 1.3 83.8 - - - +
112A MET* 1.3 57.6 + - - +
113A VAL 3.7 1.6 - - - -
63C THR* 4.1 31.2 - - + +
64C ASN* 4.1 5.4 + - + +
65C HIS* 2.8 30.3 + - - +
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.5 0.9 - - + -
43A TYR* 2.8 45.1 + - + +
45A ALA* 3.4 0.5 - - - +
91A SER 3.1 3.4 + - - -
93A ILE* 3.7 42.2 - - + +
95A ILE* 4.0 16.2 - - + -
109A TYR* 3.6 22.9 - - + +
110A GLU 3.5 9.9 - - - +
111A ASP* 1.3 77.8 - - - +
113A VAL* 1.3 61.7 + - - +
64C ASN* 3.5 28.9 - - - -
65C HIS* 3.4 17.7 - - - -
68C ILE* 4.1 15.0 - - + -
53E LEU* 4.3 11.4 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.0 0.2 - - - +
43A TYR* 3.6 5.2 - - + -
44A GLU 3.6 25.1 - - - +
45A ALA 3.6 2.5 - - - -
46A PHE* 4.0 11.9 - - + -
90A LEU* 3.0 8.7 - - - -
91A SER* 2.8 48.8 + - - +
92A PRO 4.8 0.9 - - - +
93A ILE* 3.5 27.4 - - + -
112A MET* 1.3 81.9 - - - +
114A VAL* 1.3 72.5 + - - +
115A GLU* 3.4 8.0 + - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 2.8 45.1 + - + -
45A ALA 2.9 11.9 + - - +
46A PHE* 3.7 15.1 - - + +
47A HIS* 4.4 2.7 - - - -
48A CYS* 3.7 17.3 - - - -
87A PRO* 3.6 21.1 - - + -
89A ARG 4.0 4.0 - - - -
90A LEU* 4.1 2.2 - - + -
112A MET 4.3 0.2 - - - -
113A VAL* 1.3 71.2 - - - +
115A GLU* 1.3 54.5 + - - +
116A SER 3.7 19.7 - - - +
117A CYS* 4.0 0.9 - - - -
65C HIS* 3.3 36.6 - - + +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.6 23.6 + - - +
89A ARG* 2.9 52.6 + - - +
90A LEU 4.2 0.4 - - - -
91A SER* 2.5 41.8 + - - +
113A VAL* 3.8 7.9 - - - +
114A VAL* 1.3 76.9 - - - +
116A SER* 1.3 63.6 + - - +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 4.9 3.8 - - - +
87A PRO* 3.5 5.5 - - - +
88A THR* 3.0 37.7 + - - -
89A ARG* 3.3 24.4 + - - +
114A VAL* 3.7 5.2 - - - +
115A GLU* 1.3 81.5 - - - +
117A CYS* 1.3 67.9 + - - +
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Residues in contact with CYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS* 4.0 13.7 - - - +
20A SER* 4.0 9.6 - - - -
21A ARG* 3.5 31.0 - - - +
48A CYS* 2.1 54.1 - - + -
60A LEU* 4.5 13.0 - - - +
86A VAL 3.4 5.6 - - - -
88A THR* 3.7 9.7 + - - -
114A VAL* 4.0 1.6 - - - -
116A SER* 1.3 76.9 - - - +
118A GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS* 3.6 12.7 - - - -
60A LEU* 4.6 11.7 - - - -
84A CYS 3.3 2.6 - - - +
85A CYS* 3.5 0.3 - - - -
86A VAL* 3.0 34.7 + - - +
88A THR* 3.5 12.1 - - - +
117A CYS* 1.3 78.4 - - - +
119A CYS* 1.3 61.8 + - - -
120A ARG* 3.6 6.3 + - - -
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.3 5.2 - - - -
19A CYS* 3.9 13.5 - - - -
52A CYS* 2.1 49.4 - - - -
56A LEU* 4.0 19.1 - - + -
60A LEU* 4.0 14.5 - - + +
62A PRO* 3.9 4.2 - - + +
66A ALA* 3.5 15.7 - - + +
83A THR* 3.4 13.7 - - - +
84A CYS 3.5 4.3 - - - -
118A GLY* 1.3 71.9 - - - -
120A ARG* 1.3 79.9 + - - +
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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