Contacts of the strand formed by residues 104 - 120 (chain C) in PDB entry 3QB4
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.0 22.2 - - + -
96C LEU* 3.7 33.5 - - + +
97C PHE 3.6 3.8 - - - +
98C ILE* 4.7 7.9 - - + -
102C ASN 5.6 1.1 - - - +
103C ASN* 1.3 79.2 + - - +
105C VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE 3.6 0.5 - - - +
96C LEU* 3.2 8.9 - - - +
97C PHE* 2.8 68.3 + - + +
99C ASP* 4.8 12.8 - - + +
103C ASN 3.5 2.5 + - - +
104C VAL* 1.3 76.3 - - - +
106C TYR* 1.3 83.2 + - + +
107C LYS* 5.3 1.3 - - + -
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C SER* 3.4 38.4 + - - -
95C ILE 3.4 12.3 - - - -
96C LEU* 4.1 19.7 - - + -
105C VAL* 1.3 97.0 - - + +
107C LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 107 (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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80B TYR* 5.6 7.3 + - - -
84B ASP* 4.0 5.8 + - - -
94C SER* 3.4 3.7 - - - -
95C ILE 3.0 29.9 + - - +
97C PHE* 3.7 27.8 - - + -
105C VAL* 5.3 2.0 - - + -
106C TYR* 1.3 78.0 - - - +
108C GLN* 1.3 77.5 + - - +
109C TYR* 3.2 42.7 + - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PRO* 3.6 30.9 - - + +
93C ILE 3.8 5.3 - - - +
94C SER* 4.0 15.3 + - - +
106C TYR* 6.0 0.2 - - - -
107C LYS* 1.3 88.6 + - - +
109C TYR* 1.3 64.0 + - - +
110C GLU* 2.9 30.6 + - - +
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Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 3.9 12.6 - - - +
81B GLU* 6.0 0.2 - - - -
84B ASP* 2.6 33.7 + - - -
85B PHE* 3.7 32.3 - + - -
36C TRP* 3.9 14.3 - + - -
92C PRO* 2.9 26.4 - - - +
93C ILE 2.7 19.5 + - - +
95C ILE* 3.8 31.4 - - + -
97C PHE* 4.3 6.7 - + - -
107C LYS* 3.2 43.9 + - + -
108C GLN* 1.3 76.0 - - - +
110C GLU* 1.3 61.7 + - - +
112C MET* 3.3 20.5 - - + +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 2.8 25.5 + - - +
81B GLU* 3.8 14.1 + - - +
92C PRO* 3.8 15.8 - - - +
108C GLN* 2.9 37.4 + - - +
109C TYR* 1.3 73.8 - - - +
111C ASP* 1.3 85.4 + - - +
112C MET* 3.3 1.4 + - - +
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Residues in contact with ASP 111 (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* 3.7 35.6 - - + +
64A ASN 4.2 1.8 - - - +
65A HIS* 2.8 29.1 + - - +
81B GLU* 4.1 8.0 - - - +
90C LEU* 3.6 35.0 + - + +
91C SER* 3.7 10.3 + - - +
110C GLU* 1.3 86.7 + - - +
112C MET* 1.3 59.5 + - - +
113C VAL 3.7 1.3 - - - -
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Residues in contact with MET 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 3.6 25.8 - - - -
65A HIS* 3.5 17.9 - - - +
68A ILE* 4.8 4.3 - - + -
85B PHE* 4.1 15.3 - - + -
28C PHE* 4.5 2.9 - - + -
43C TYR* 2.8 52.3 + - + +
45C ALA* 3.5 1.2 - - - +
91C SER 3.0 7.0 + - - +
93C ILE* 3.7 33.4 - - + +
95C ILE* 4.2 14.1 - - + -
109C TYR* 3.3 33.0 - - + +
110C GLU 3.5 3.8 - - - +
111C ASP* 1.3 77.3 - - - +
113C VAL* 1.3 59.7 + - - +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG* 4.9 0.2 - - - +
43C TYR* 3.9 2.5 - - + -
44C GLU 3.7 24.0 - - - +
45C ALA 3.6 2.7 - - - -
46C PHE* 3.8 14.4 - - + -
90C LEU* 3.2 7.1 - - - -
91C SER* 2.9 40.3 + - - +
92C PRO 4.7 0.7 - - - +
93C ILE* 3.5 28.9 - - + -
111C ASP 3.7 0.2 - - - -
112C MET* 1.3 83.3 - - - +
114C VAL* 1.3 77.2 + - - +
115C GLU* 3.3 11.4 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 3.4 28.9 - - + +
21C ARG* 2.7 48.5 + - + -
45C ALA 2.9 14.1 + - - +
46C PHE* 3.7 14.7 - - + +
47C HIS* 4.4 3.1 - - - +
48C CYS* 3.8 22.2 - - - -
87C PRO* 3.6 27.4 - - + -
89C ARG 4.0 3.1 - - - +
90C LEU* 4.1 2.9 - - + -
113C VAL* 1.3 74.5 - - - +
115C GLU* 1.3 54.7 + - - +
116C SER 3.8 12.1 - - - +
117C CYS* 3.9 0.4 - - - -
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG* 3.8 22.3 + - - +
89C ARG* 2.8 49.9 + - - +
90C LEU 4.0 1.8 - - - -
91C SER* 2.5 45.3 + - - +
113C VAL* 3.3 9.4 + - - +
114C VAL* 1.3 78.1 - - - +
116C SER* 1.3 61.1 + - - +
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Residues in contact with SER 116 (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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21C ARG* 5.0 2.5 - - - +
59C HIS 5.5 3.4 - - - -
61C GLU* 4.7 6.3 + - - -
87C PRO* 3.5 5.5 - - - +
88C THR* 2.8 38.5 + - - -
89C ARG* 3.3 32.5 + - - +
114C VAL* 3.8 3.0 - - - +
115C GLU* 1.3 80.4 - - - +
117C CYS* 1.3 63.0 + - - +
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Residues in contact with CYS 117 (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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19C CYS* 4.1 13.7 - - - -
20C SER* 3.7 11.0 - - - -
21C ARG* 3.6 28.9 - - - +
47C HIS 4.0 0.2 - - - -
48C CYS* 2.0 55.0 - - + -
59C HIS* 3.6 17.8 - - - +
60C LEU* 4.1 6.9 - - - +
86C VAL 3.4 5.8 - - - -
88C THR* 3.6 4.8 + - - -
114C VAL* 3.9 2.5 - - - -
116C SER* 1.3 76.0 - - - +
118C GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 118 (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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19C CYS* 3.9 9.6 - - - -
60C LEU* 3.3 19.3 - - - -
84C CYS 3.4 1.2 - - - +
85C CYS* 3.4 2.4 - - - -
86C VAL* 2.9 35.7 + - - +
88C THR* 3.5 16.4 - - - +
117C CYS* 1.3 75.8 - - - +
119C CYS* 1.3 60.3 + - - -
120C ARG 3.9 0.3 + - - -
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Residues in contact with CYS 119 (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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19C CYS* 3.9 8.7 - - - -
52C CYS* 2.0 54.3 - - + -
56C LEU* 3.9 16.6 - - + -
60C LEU* 3.2 33.3 + - + +
62C PRO* 3.6 13.4 - - + +
66C ALA* 3.7 5.8 - - - +
83C THR* 3.9 6.5 - - - +
84C CYS 3.5 4.3 - - - -
118C GLY* 1.3 71.7 - - - -
120C ARG* 1.3 72.8 + - - +
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Residues in contact with ARG 120 (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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86A VAL* 3.7 22.6 - - + +
87A PRO* 3.4 34.3 - - + +
60C LEU 3.4 6.7 + - - -
61C GLU* 2.4 43.6 + - - +
62C PRO* 3.7 1.0 - - - +
63C THR* 4.0 28.2 + - - +
65C HIS* 4.7 3.1 + - - -
66C ALA* 3.8 15.6 - - - +
69C GLN* 5.2 1.2 - - - +
83C THR* 3.3 15.3 - - - +
84C CYS* 3.0 27.9 + - - +
86C VAL* 3.8 26.2 - - + -
88C THR* 3.4 31.8 + - + +
119C CYS* 1.3 84.6 + - - +
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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