Contacts of the strand formed by residues 85 - 98 (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 CYS 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B CYS* 4.8 1.9 - - - +
19D CYS* 2.1 51.4 - - + -
20D SER 3.7 3.1 - - - -
48D CYS* 3.8 18.2 - - - +
49D GLU* 3.5 22.4 - - - +
50D GLY 3.4 24.8 + - - +
52D CYS* 3.5 4.6 - - - -
84D CYS* 1.3 76.6 - - - +
86D VAL* 1.3 64.8 + - - +
117D CYS* 4.2 0.7 - - - -
118D GLY 3.5 4.9 - - - -
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Residues in contact with VAL 86 (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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84B CYS* 3.8 17.5 - - + -
86B VAL* 3.6 34.1 - - + -
120B ARG* 3.8 14.8 - - + +
48D CYS* 3.4 8.3 - - - -
84D CYS 3.9 2.2 - - - +
85D CYS* 1.3 80.5 - - - +
87D PRO* 1.3 85.0 - - + +
88D THR* 3.6 0.5 - - - +
117D CYS* 3.4 1.0 - - - -
118D GLY 3.0 31.4 + - - +
120D ARG* 3.8 31.6 - - + -
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Residues in contact with PRO 87 (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* 6.1 0.7 - - - +
65B HIS* 4.4 7.2 - - + +
69B GLN* 5.8 0.9 - - - +
120B ARG* 3.4 32.1 - - + +
48D CYS* 3.4 11.2 - - + +
86D VAL* 1.3 98.3 - - + +
88D THR* 1.3 62.1 + - - +
90D LEU* 3.8 32.5 - - + +
114D VAL* 3.6 26.9 - - + -
116D SER 3.5 9.0 - - - +
120D ARG* 5.3 0.7 - - - +
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Residues in contact with THR 88 (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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86D VAL 3.6 2.0 - - - +
87D PRO* 1.3 78.6 - - - +
89D ARG* 1.3 72.3 + - - +
90D LEU* 5.1 2.7 - - - -
116D SER* 3.0 25.8 + - - -
117D CYS 3.7 5.0 + - - -
118D GLY* 3.6 31.0 - - - +
120D ARG* 3.7 36.3 - - + +
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Residues in contact with ARG 89 (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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60D LEU* 5.0 5.5 + - - +
61D GLU* 3.8 20.0 + - - -
88D THR* 1.3 86.5 + - - +
90D LEU* 1.3 69.9 + - - +
114D VAL* 3.9 0.7 - - - -
115D GLU* 2.9 40.3 + - + -
116D SER* 2.9 33.4 + - - +
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Residues in contact with LEU 90 (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* 4.8 12.3 - - + -
65B HIS* 3.9 28.5 - - + -
87D PRO* 3.8 28.7 - - + +
88D THR 5.1 2.2 - - - -
89D ARG* 1.3 83.7 - - - +
91D SER* 1.3 61.4 + - - +
92D PRO* 4.9 0.2 - - - +
111D ASP* 3.8 39.8 + - + +
113D VAL 3.1 15.0 - - - +
114D VAL* 4.1 7.9 - - + -
115D GLU* 4.1 4.0 - - - +
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Residues in contact with SER 91 (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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90D LEU* 1.3 76.0 - - - +
92D PRO* 1.3 78.5 + - - +
111D ASP 4.3 3.6 - - - -
112D MET 3.1 6.9 + - - -
113D VAL* 2.8 44.1 + - - +
115D GLU* 4.9 9.2 - - - -
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Residues in contact with PRO 92 (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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91D SER* 1.3 100.2 + - - +
93D ILE* 1.3 65.4 + - - +
108D GLN* 3.5 35.9 - - + +
109D TYR 3.1 23.6 - - - +
110D GLU* 4.1 7.6 - - - -
111D ASP 4.4 0.4 - - - +
112D MET 4.6 0.2 - - - +
113D VAL* 4.7 0.9 - - - +
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Residues in contact with ILE 93 (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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28D PHE* 4.8 0.4 - - + -
40D PRO* 4.9 7.9 - - + -
43D TYR* 3.7 38.6 - - + -
92D PRO* 1.3 79.3 - - - +
94D SER* 1.3 67.8 + - - +
95D ILE* 4.0 21.3 - - + -
108D GLN* 3.6 3.0 - - - +
109D TYR* 2.8 30.8 + - - +
112D MET* 3.8 28.5 - - + +
113D VAL* 3.5 26.5 - - + -
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Residues in contact with SER 94 (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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40D PRO* 3.5 19.2 - - - +
93D ILE* 1.3 74.7 - - - +
95D ILE* 1.3 65.5 + - - +
106D TYR* 3.4 38.4 + - - -
107D LYS 3.4 8.1 - - - -
108D GLN* 3.6 22.6 + - - +
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Residues in contact with ILE 95 (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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28D PHE* 4.0 27.1 - - + -
33D TRP* 6.4 0.4 - - + -
37D ILE* 3.7 28.0 - - + -
39D ALA 3.6 10.1 - - - +
40D PRO* 4.2 2.2 - - + -
93D ILE* 4.0 11.9 - - + -
94D SER* 1.3 81.1 - - - +
96D LEU* 1.3 71.8 + - - +
97D PHE* 3.9 10.0 - - + -
105D VAL 3.6 1.4 - - - +
106D TYR* 3.5 7.5 - - - -
107D LYS 2.9 29.1 + - - -
109D TYR* 3.8 28.9 - - + -
112D MET* 4.1 18.2 - - + -
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Residues in contact with LEU 96 (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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38D ILE* 2.8 43.2 + - + -
39D ALA* 2.6 31.2 + - + +
95D ILE* 1.3 74.4 - - - +
97D PHE* 1.3 61.1 + - - +
104D VAL* 3.9 22.7 - - + -
105D VAL 3.3 14.1 - - - +
106D TYR* 3.7 27.6 - - + -
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Residues in contact with PHE 97 (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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36D TRP* 3.2 20.6 - - + +
37D ILE* 4.1 7.0 - - + -
38D ILE* 4.1 4.0 - - - +
95D ILE* 3.9 15.5 - - + -
96D LEU* 1.3 76.6 - - - +
98D ILE* 1.3 74.4 + - - +
99D ASP* 4.1 21.1 - - + -
103D ASN 3.5 1.2 - - - +
104D VAL* 3.4 3.1 - - - -
105D VAL* 2.7 68.8 + - + +
107D LYS* 3.8 25.8 - - + -
109D TYR* 3.5 30.7 - + - -
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Residues in contact with ILE 98 (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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35D ASP 4.4 11.2 - - - +
36D TRP* 2.8 45.7 + - + +
38D ILE* 3.8 26.7 - - + -
97D PHE* 1.3 80.7 - - - +
99D ASP* 1.3 70.9 + - - +
102D ASN* 3.9 28.7 - - + +
103D ASN 3.4 6.3 - - - +
104D VAL* 4.7 10.8 - - + +
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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