Contacts of the strand formed by residues 104 - 119 (chain D) 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 VAL 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ILE* 4.7 12.6 - - + -
96D LEU* 3.9 31.2 - - + -
97D PHE 3.4 7.4 - - - +
98D ILE* 4.7 14.4 - - + +
102D ASN 3.8 4.0 + - - +
103D ASN* 1.3 72.9 - - - +
105D VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LEU* 3.3 8.7 - - - +
97D PHE* 2.7 68.2 + - + +
99D ASP* 3.9 14.8 - - + +
103D ASN* 3.7 23.6 - - + +
104D VAL* 1.3 82.3 - - - +
106D TYR* 1.3 67.6 - - - +
107D LYS* 4.6 7.4 - - + -
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER* 3.4 37.4 + - - -
95D ILE 3.5 12.1 - - - -
96D LEU* 3.7 20.4 - - + -
105D VAL* 1.3 76.8 - - - +
107D LYS* 1.3 62.9 + - - +
108D GLN 5.8 0.2 - - - -
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER* 3.4 4.2 - - - -
95D ILE 2.9 31.9 + - - +
97D PHE* 3.8 26.1 - - + -
105D VAL* 4.1 6.7 + - + -
106D TYR* 1.3 77.0 - - - +
108D GLN* 1.3 73.8 + - - +
109D TYR* 3.7 31.3 + - + -
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PRO* 3.5 32.8 - - + +
93D ILE 3.6 6.1 - - - +
94D SER* 3.6 20.4 + - - +
106D TYR* 5.8 0.6 - - - -
107D LYS* 1.3 85.3 - - - +
109D TYR* 1.3 64.8 + - - +
110D GLU* 4.1 7.0 + - - +
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Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASN* 4.3 15.5 - - - +
92D PRO* 3.1 24.1 - - - +
93D ILE 2.8 14.1 + - - +
95D ILE* 3.8 27.8 - - + -
97D PHE* 3.5 38.3 - + - -
107D LYS* 3.7 36.5 + - + +
108D GLN* 1.3 73.7 - - - +
110D GLU* 1.3 67.3 + - - +
112D MET* 3.6 24.2 - - + +
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASN* 2.4 38.5 + - - +
92D PRO* 4.1 9.4 - - + -
108D GLN* 4.1 5.5 + - - +
109D TYR* 1.3 86.0 - - - +
111D ASP* 1.3 80.7 + - - +
112D MET* 3.3 1.6 + - - +
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Residues in contact with ASP 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B THR* 4.0 31.4 - - + +
64B ASN* 3.5 5.7 + - - +
65B HIS* 2.8 29.6 + - - +
90D LEU* 3.8 32.8 + - + +
91D SER 3.9 8.5 + - - +
110D GLU* 1.3 87.9 - - - +
112D MET* 1.3 59.2 + - - +
113D VAL 3.7 0.9 - - - -
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Residues in contact with MET 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASN* 3.4 28.7 - - - -
65B HIS* 3.4 17.7 - - - +
68B ILE* 4.0 15.3 - - + -
28D PHE* 4.5 1.1 - - + -
33D TRP* 6.0 0.4 - - + -
43D TYR* 2.8 44.8 + - + +
45D ALA* 3.4 0.7 - - - +
91D SER 3.1 3.4 + - - -
93D ILE* 3.8 41.1 - - + +
95D ILE* 4.1 17.7 - - + -
109D TYR* 3.6 27.4 - - + +
110D GLU 3.5 10.3 - - - +
111D ASP* 1.3 76.6 - - - +
113D VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 5.0 1.3 - - - +
43D TYR* 3.6 4.7 - - + -
44D GLU 3.6 25.8 - - - +
45D ALA 3.6 2.2 - - - -
46D PHE* 4.0 11.7 - - + -
90D LEU* 3.1 8.2 - - - -
91D SER* 2.8 44.3 + - - +
92D PRO 4.7 2.0 - - - +
93D ILE* 3.5 28.0 - - + -
112D MET* 1.3 83.4 - - - +
114D VAL* 1.3 74.3 + - - +
115D GLU* 3.4 1.7 + - + -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.4 31.0 - - + +
21D ARG* 2.8 44.7 + - + -
45D ALA 2.9 12.5 + - - +
46D PHE* 3.7 15.9 - - + +
47D HIS* 4.4 3.1 - - - -
48D CYS* 3.7 16.6 - - - -
87D PRO* 3.6 26.2 - - + -
89D ARG 4.0 3.1 - - - -
90D LEU* 4.1 3.6 - - + -
112D MET 4.2 0.2 - - - -
113D VAL* 1.3 72.5 - - - +
115D GLU* 1.3 53.7 + - - +
116D SER 3.7 19.7 - - - +
117D CYS* 4.0 1.3 - - - -
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 3.6 24.1 + - - +
89D ARG* 2.9 35.0 + - + +
90D LEU* 4.6 5.2 - - - -
91D SER* 4.9 7.9 - - - -
113D VAL* 3.4 5.9 + - + +
114D VAL* 1.3 73.0 - - - +
116D SER* 1.3 60.6 + - - +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 4.9 3.8 - - - +
87D PRO* 3.5 6.2 - - - +
88D THR* 3.0 35.5 + - - -
89D ARG* 2.9 44.5 + - - +
114D VAL* 3.7 5.1 - - - +
115D GLU* 1.3 79.6 - - - +
117D CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D CYS* 4.0 14.4 - - - -
20D SER* 3.7 10.5 - - - -
21D ARG* 3.5 30.6 - - - +
48D CYS* 2.1 54.1 - - + -
60D LEU* 4.0 21.8 - - - +
86D VAL 3.4 4.5 - - - -
88D THR* 3.7 9.5 + - - -
114D VAL* 4.0 1.8 - - - -
116D SER* 1.3 76.7 - - - +
118D GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D CYS* 3.6 12.6 - - - -
60D LEU* 4.4 11.9 - - - -
84D CYS 3.3 2.3 - - - +
85D CYS* 3.5 0.2 - - - -
86D VAL* 3.0 34.8 + - - +
88D THR* 3.6 11.4 - - - -
117D CYS* 1.3 78.0 - - - +
119D CYS* 1.3 62.8 + - - -
120D ARG* 3.6 6.5 + - - -
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Residues in contact with CYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 4.3 5.2 - - - -
19D CYS* 3.9 13.7 - - - -
52D CYS* 2.1 49.4 - - - -
56D LEU* 4.0 18.8 - - + -
60D LEU* 5.0 7.2 - - - +
62D PRO* 3.9 8.0 - - + +
66D ALA* 3.5 15.4 - - + +
83D THR* 3.5 13.2 - - - +
84D CYS 3.5 4.5 - - - -
118D GLY* 1.3 70.5 - - - -
120D ARG* 1.3 81.7 + - - +
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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