Contacts of the strand formed by residues 85 - 98 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A CYS* 4.8 1.7 - - - +
19C CYS* 2.1 52.5 - - + -
20C SER 3.7 2.7 - - - -
48C CYS* 3.8 17.5 - - - +
49C GLU* 3.5 22.6 - - - -
50C GLY 3.4 24.8 + - - +
52C CYS* 3.5 5.0 - - - +
84C CYS* 1.3 78.5 - - - +
86C VAL* 1.3 64.7 + - - +
117C CYS* 4.2 0.2 - - - -
118C GLY 3.5 5.2 - - - -
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A CYS* 3.8 10.5 - - + -
86A VAL* 3.6 33.7 - - + -
120A ARG* 3.8 22.4 - - + +
48C CYS* 3.5 8.7 - - - -
84C CYS 3.9 1.8 - - - +
85C CYS* 1.3 81.1 - - - +
87C PRO* 1.3 81.5 - - + +
88C THR* 3.6 0.3 - - - +
117C CYS* 3.4 1.0 - - - -
118C GLY 3.0 32.5 + - - +
120C ARG* 3.8 31.4 - - + -
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Residues in contact with PRO 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 6.1 0.4 - - - +
65A HIS* 4.5 6.7 - - + +
69A GLN* 5.9 0.2 - - - +
120A ARG* 3.4 31.3 - - + +
48C CYS* 3.6 11.0 - - + +
86C VAL* 1.3 99.3 - - + +
88C THR* 1.3 60.5 + - - +
90C LEU* 3.8 32.6 - - + +
114C VAL* 3.6 26.5 - - + -
116C SER 3.5 9.2 - - - +
120C ARG* 5.4 0.2 - - - +
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL 3.6 2.0 - - - +
87C PRO* 1.3 79.0 - - - +
89C ARG* 1.3 73.7 + - - +
90C LEU* 5.2 2.2 - - - -
116C SER* 3.0 25.4 + - - -
117C CYS 3.7 5.0 + - - -
118C GLY* 3.6 31.6 - - - +
120C ARG* 3.7 38.9 + - + +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 5.0 10.1 + - - -
88C THR* 1.3 88.3 + - - +
90C LEU* 1.3 70.4 + - - +
114C VAL* 4.0 0.7 - - - +
115C GLU* 2.9 36.1 + - + -
116C SER* 2.9 57.1 + - - +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 4.8 12.1 - - + +
65A HIS* 3.9 28.3 - - + -
87C PRO* 3.8 30.7 - - + +
88C THR 5.2 0.9 - - - -
89C ARG* 1.3 83.8 - - - +
91C SER* 1.3 61.3 + - - +
111C ASP* 3.8 40.4 + - + +
113C VAL 3.1 15.5 - - - +
114C VAL* 4.1 7.6 - - + -
115C GLU* 4.1 4.3 - - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 1.3 73.8 - - - +
92C PRO* 1.3 75.8 + - - +
111C ASP 4.4 2.9 - - - -
112C MET 3.1 7.5 + - - -
113C VAL* 2.8 40.1 + - - +
115C GLU* 2.5 32.9 + - - -
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Residues in contact with PRO 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 1.3 94.1 + - - +
93C ILE* 1.3 67.2 + - - +
108C GLN* 3.5 35.7 - - + +
109C TYR 3.1 22.9 - - - +
110C GLU* 4.1 7.9 - - + -
111C ASP 4.5 0.6 - - - +
112C MET 4.6 0.4 - - - +
113C VAL* 4.8 0.5 - - - +
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 4.8 0.7 - - + -
40C PRO* 4.9 7.9 - - + -
43C TYR* 3.7 38.8 - - + -
92C PRO* 1.3 79.5 - - - +
94C SER* 1.3 67.3 + - - +
95C ILE* 4.0 20.4 - - + -
108C GLN* 3.6 3.5 - - - +
109C TYR* 2.8 30.7 + - - +
112C MET* 3.8 27.8 - - + +
113C VAL* 3.5 26.7 - - + -
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PRO* 3.5 19.2 - - - +
93C ILE* 1.3 77.9 - - - +
95C ILE* 1.3 63.5 + - - +
106C TYR* 3.4 38.0 + - - -
107C LYS 3.4 7.2 - - - -
108C GLN* 3.6 22.6 + - - +
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 4.0 27.6 - - + -
37C ILE* 3.7 28.9 - - + -
39C ALA 3.6 11.0 - - - +
40C PRO* 4.2 1.8 - - + -
93C ILE* 4.0 12.1 - - + -
94C SER* 1.3 78.6 - - - +
96C LEU* 1.3 72.4 + - - +
97C PHE* 3.9 9.5 - - + -
105C VAL 3.6 1.4 - - - +
106C TYR* 3.5 6.9 - - - -
107C LYS 2.9 29.6 + - - +
109C TYR* 3.8 28.0 - - + -
112C MET* 4.1 18.2 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 2.8 42.7 + - + -
39C ALA* 2.6 31.3 + - + +
95C ILE* 1.3 74.4 - - - +
97C PHE* 1.3 61.3 + - - +
104C VAL* 3.9 22.4 - - + -
105C VAL* 3.3 14.4 - - - +
106C TYR* 3.7 27.3 - - + -
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Residues in contact with PHE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C TRP* 3.2 19.7 - - + +
37C ILE* 4.1 6.3 - - + -
38C ILE* 4.1 4.9 - - - +
95C ILE* 3.9 16.6 - - + -
96C LEU* 1.3 75.3 - - - +
98C ILE* 1.3 75.4 + - - +
99C ASP* 4.1 20.6 - - + -
103C ASN 3.5 1.2 - - - +
104C VAL* 3.4 3.0 - - - -
105C VAL* 2.7 68.5 + - + +
107C LYS* 3.8 26.9 - - + -
109C TYR* 3.5 31.2 - + - -
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASP 4.4 10.8 - - - +
36C TRP* 2.8 45.6 + - + +
38C ILE* 3.8 26.9 - - + -
97C PHE* 1.3 81.7 - - - +
99C ASP* 1.3 72.6 + - - +
102C ASN* 3.8 31.2 - - - +
103C ASN 3.4 6.3 - - - +
104C VAL* 5.1 9.6 - - + -
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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