Contacts of the strand formed by residues 104 - 114 (chain C) in PDB entry 1QZH
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 PRO 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C PHE* 4.5 4.0 - - + -
47C GLY 3.2 8.3 - - - +
48C ILE* 3.6 19.7 - - + -
102C GLY 3.6 2.9 - - - +
103C GLN* 1.3 84.2 - - - +
105C LEU* 1.3 60.6 + - - +
131C LEU* 3.3 4.2 - - - +
132C TRP* 3.1 43.0 + - + +
133C PRO 3.4 19.7 - - - +
135C PHE* 4.4 1.1 - - + -
162C ALA* 3.7 37.7 - - + +
165C LEU* 5.2 1.1 - - + -
166C ASN* 4.0 8.1 - - + +
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Residues in contact with LEU 105 (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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45C LEU 4.1 0.2 - - - +
46C PHE* 3.4 5.8 - - - -
47C GLY 2.6 34.7 + - - +
49C VAL* 3.9 26.9 - - + -
69C VAL* 4.2 24.7 - - + -
71C LEU* 4.2 11.8 - - + +
87C LEU* 5.1 3.4 - - + -
96C PRO* 4.8 5.4 - - + -
98C ILE* 4.8 2.7 - - + -
103C GLN 3.7 0.2 + - - -
104C PRO* 1.3 75.4 - - - +
106C LEU* 1.3 60.6 + - - +
107C LEU* 3.9 32.3 + - + -
129C TYR* 4.0 20.0 - - + -
130C ALA 3.2 16.8 - - - +
131C LEU* 4.1 13.0 - - + -
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Residues in contact with LEU 106 (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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25C LEU* 4.8 2.5 - - + -
27C PHE* 3.7 35.4 - - + -
45C LEU 3.5 2.9 - - - -
46C PHE* 3.9 23.1 - - + -
105C LEU* 1.3 72.0 - - - +
107C LEU* 1.3 71.6 + - - +
108C HIS* 4.2 2.7 - - + +
129C TYR* 3.0 9.4 - - - +
130C ALA* 2.9 40.7 + - + -
132C TRP* 3.8 25.2 - - + -
152C MET* 4.0 31.2 - - + -
154C THR* 4.7 3.4 - - + -
158C GLU* 4.5 11.0 - - + +
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Residues in contact with LEU 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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44C ASN* 3.3 7.6 - - - +
45C LEU* 2.9 41.9 + - + +
69C VAL* 4.7 1.8 - - + -
71C LEU* 4.4 6.3 - - + -
85C ILE* 3.5 38.8 - - + -
87C LEU* 4.0 20.0 - - + -
105C LEU* 3.9 30.9 + - + -
106C LEU* 1.3 76.4 - - - +
108C HIS* 1.3 60.4 + - - +
109C GLN 4.1 0.2 - - - -
110C ILE* 3.7 24.0 - - + -
127C PHE* 4.3 7.9 - - + -
128C ARG 3.9 0.7 - - - +
129C TYR* 3.9 21.1 - - + -
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Residues in contact with HIS 108 (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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25C LEU* 3.9 27.1 - - + +
44C ASN* 2.8 30.9 + - - -
106C LEU* 4.2 2.7 + - + -
107C LEU* 1.3 71.9 - - - +
109C GLN* 1.3 98.0 + - + +
110C ILE* 4.9 0.8 - - - +
126C GLN 5.2 1.0 + - - -
127C PHE* 3.2 6.0 - - - +
128C ARG* 3.0 49.5 + - + +
152C MET* 4.0 19.4 - - + +
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Residues in contact with GLN 109 (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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42C ILE* 3.5 29.1 + - - +
43C VAL 3.3 6.6 + - - -
44C ASN* 3.2 12.9 + - - +
108C HIS* 1.3 109.3 + - + +
110C ILE* 1.3 66.0 + - - +
124C LYS* 3.1 40.0 + - + +
126C GLN* 3.7 23.0 + - - +
127C PHE* 3.6 8.2 - - - +
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Residues in contact with ILE 110 (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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42C ILE* 3.5 2.8 - - - +
43C VAL* 2.9 41.6 + - + +
45C LEU* 4.4 19.1 - - + -
85C ILE* 4.1 7.4 - - + -
87C LEU* 4.0 12.3 - - + -
107C LEU* 3.7 42.4 - - + +
108C HIS 4.9 0.2 - - - -
109C GLN* 1.3 84.8 - - - +
111C THR* 1.3 64.8 + - - +
112C LEU* 3.7 3.4 + - + -
121C GLY* 3.8 27.4 - - - -
122C LEU 3.8 5.6 - - - +
123C SER* 3.9 16.4 - - - -
127C PHE* 4.6 6.1 - - + -
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Residues in contact with THR 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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40C ASN* 3.8 23.1 - - + +
41C THR 3.5 7.6 - - - +
42C ILE* 4.1 6.3 - - + +
109C GLN 4.3 0.4 + - - -
110C ILE* 1.3 70.6 - - - +
112C LEU* 1.3 74.8 + - - +
113C ARG* 3.7 4.3 + - + +
120C GLN 3.5 1.0 - - - +
121C GLY* 3.5 2.9 - - - -
122C LEU* 2.7 41.2 + - - +
124C LYS* 3.3 15.4 + - - +
2I G 2.9 39.2 + - + +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C GLN* 5.1 1.8 - - + -
33C SER* 3.9 37.9 - - - +
37C GLN* 4.8 6.2 - - + +
39C LYS 4.3 2.4 - - - +
40C ASN* 3.4 23.2 - - - -
41C THR* 3.0 21.5 + - - +
43C VAL* 3.8 40.6 - - + -
45C LEU* 4.9 0.2 - - + -
83C LEU* 4.4 23.1 - - + -
110C ILE* 3.7 4.0 + - + -
111C THR* 1.3 74.6 - - - +
113C ARG* 1.3 65.0 + - - +
119C THR* 4.1 8.3 - - + -
120C GLN 3.7 2.0 - - - +
121C GLY* 4.6 9.4 - - - -
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Residues in contact with ARG 113 (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 LEU* 6.0 0.2 - - - -
37C GLN 4.7 7.6 - - - -
38C LYS 5.7 0.2 - - - -
40C ASN* 3.9 24.0 - - - +
111C THR* 4.4 5.2 - - + +
112C LEU* 1.3 77.4 - - - +
114C SER* 1.3 76.8 + - - +
115C TYR* 4.2 11.5 - - - +
119C THR* 3.4 7.3 - - - +
120C GLN* 2.7 58.6 + - - +
122C LEU* 3.0 33.6 - - + +
2I G 4.0 19.2 + - + +
3I T 4.4 2.6 + - - -
5I A 3.3 32.9 + - - +
6I C 3.3 11.3 - - - +
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Residues in contact with SER 114 (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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31A ARG* 2.8 35.5 + - - -
77A ASP* 4.5 9.0 + - - -
36C LEU* 4.6 2.0 - - - -
37C GLN 5.0 2.3 + - - -
38C LYS* 5.9 1.5 + - - -
40C ASN* 5.5 0.2 - - - +
113C ARG* 1.3 98.5 + - - +
115C TYR* 1.3 62.2 + - - +
116C ARG 4.5 0.5 + - - -
117C ASP* 3.7 19.6 + - - -
118C ARG 3.4 5.6 - - - -
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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