Contacts of the strand formed by residues 113 - 122 (chain H) in PDB entry 1U3H
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 ASN 113 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103H LEU* 3.9 17.2 - - + +
105H ARG* 3.0 39.2 - - + +
106H THR* 3.9 13.3 + - - +
111H HIS* 3.4 28.1 - - - +
112H HIS* 1.3 81.4 + - - +
114H THR* 1.3 69.9 + - - +
162H GLU* 3.5 6.1 - - - +
163H MET* 3.0 31.1 + - - +
165H PRO* 3.4 26.7 - - - +
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Residues in contact with THR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H LEU* 3.6 5.8 - - - -
104H SER* 2.9 41.5 + - - +
105H ARG* 4.3 4.5 - - - +
113H ASN* 1.3 79.8 + - - +
115H LEU* 1.3 76.5 + - - +
116H VAL* 4.1 4.5 - - + -
160H MET* 3.7 27.4 - - + -
161H LEU 3.5 8.1 - - - +
162H GLU* 2.8 27.4 + - - +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ILE* 4.5 1.3 - - + -
102H SER 3.4 8.3 - - - +
103H LEU* 3.4 26.0 - - + -
114H THR* 1.3 79.9 - - - +
116H VAL* 1.3 61.3 + - - +
131H TRP* 3.7 23.2 - - + -
159H VAL 3.9 0.7 - - - +
160H MET* 3.4 1.0 - - - -
161H LEU* 3.0 36.7 + - + +
163H MET* 3.6 21.1 - - + +
171H TYR* 3.6 43.1 - - + -
188H TRP* 3.9 34.1 - - + +
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Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H VAL 3.5 2.3 - - - +
101H ILE* 3.4 3.8 - - - -
102H SER* 2.7 44.0 + - - +
104H SER* 3.9 21.1 - - - +
114H THR* 4.1 4.5 - - + +
115H LEU* 1.3 79.0 - - - +
117H CYS* 1.3 65.3 - - - +
118H SER* 3.6 17.4 + - - +
131H TRP* 4.0 3.1 - - - -
158H LEU* 4.4 19.3 - - + -
159H VAL 3.5 6.3 - - - +
160H MET* 3.8 20.6 - - + -
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Residues in contact with CYS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 3.6 20.4 - - - -
100H VAL 3.6 4.7 - - - -
101H ILE* 4.5 2.9 - - + +
116H VAL* 1.3 73.4 - - - +
118H SER* 1.3 59.0 + - - +
119H VAL* 3.6 12.4 + - - +
129H VAL* 4.8 0.2 - - + -
131H TRP* 3.5 19.2 - - + +
157H VAL 3.8 0.9 - - - +
158H LEU* 3.7 1.0 - - - -
159H VAL* 2.7 38.4 + - + +
173H CYS* 2.0 49.4 - - + -
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Residues in contact with SER 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO* 3.7 31.4 - - - +
98H ASN 3.0 12.0 - - - +
99H VAL* 3.4 1.6 - - - -
100H VAL* 2.9 29.8 + - - +
102H SER* 5.0 3.6 + - - -
116H VAL* 3.6 11.3 + - - +
117H CYS* 1.3 70.8 - - - +
119H VAL* 1.3 60.3 + - - +
120H THR* 3.8 5.4 - - - +
158H LEU* 3.7 24.8 - - - +
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Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PRO* 3.8 19.1 - - + -
98H ASN 3.2 4.7 - - - +
99H VAL* 4.4 3.1 - - + -
117H CYS* 3.9 19.7 - - - +
118H SER* 1.3 76.1 - - - +
120H THR* 1.3 60.9 + - - +
122H PHE* 3.0 19.1 - - + -
127H ILE* 3.3 33.2 - - + -
129H VAL* 4.0 12.6 - - + -
157H VAL* 3.0 31.3 + - + +
175H VAL* 3.8 27.1 - - + -
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Residues in contact with THR 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G LYS 3.8 20.8 + - - +
95G SER* 4.4 0.7 - - - -
96G PRO* 3.8 25.6 - - + +
97H PRO* 3.6 1.7 - - - +
98H ASN* 2.7 50.5 + - - +
118H SER* 4.2 8.7 - - - -
119H VAL* 1.3 84.6 - - - +
121H ASP* 1.3 76.5 + - - +
122H PHE* 3.3 3.8 + - - -
155H PHE 3.6 4.0 - - - -
156H GLN* 3.7 19.5 - - + +
158H LEU* 5.1 0.7 - - + -
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Residues in contact with ASP 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G LYS* 2.8 44.0 + - - +
95G SER* 3.6 12.0 + - - -
95H GLU* 3.3 20.1 - - - +
96H GLN 3.8 8.9 - - - +
98H ASN* 4.1 14.6 + - + +
120H THR* 1.3 86.4 + - - +
122H PHE* 1.3 60.2 + - - +
150H ASN* 4.6 1.9 + - - +
154H THR* 3.7 17.4 + - + +
155H PHE 2.9 10.2 + - - -
156H GLN* 4.6 0.4 - - - +
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Residues in contact with PHE 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H GLU 3.3 4.7 - - - -
97H PRO* 3.3 31.0 - - + -
119H VAL* 3.0 32.3 - - + -
120H THR 4.0 4.5 - - - -
121H ASP* 1.3 80.0 - - - +
123H TYR* 1.3 64.9 + - - +
124H PRO 3.4 14.1 - - - -
125H ALA 3.5 21.5 - - - -
127H ILE* 3.7 33.7 - - + -
147H LEU* 3.8 15.0 - - + -
154H THR* 3.3 2.8 - - - -
155H PHE* 2.9 48.7 + - + -
156H GLN* 3.6 4.5 - - - -
157H VAL* 4.0 5.6 - - + -
177H HIS* 3.7 8.3 - + + -
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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