Contacts of the strand formed by residues 155 - 163 (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 PHE 155 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G ASP 5.5 0.2 - - - -
29G ASP* 4.5 1.6 - - - -
121H ASP* 2.9 24.8 + - - -
122H PHE* 2.9 41.3 + - + -
123H TYR* 3.6 26.5 - + - -
124H PRO 4.1 1.1 - - - -
125H ALA* 3.7 30.1 - - + -
147H LEU* 3.6 30.5 - - + -
148H ILE 3.2 18.6 - - - +
149H ARG* 3.8 52.3 - - + -
150H ASN* 3.8 3.5 - - - +
154H THR* 1.3 77.5 - - - +
156H GLN* 1.3 62.4 + - - +
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Residues in contact with GLN 156 (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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92G PHE* 3.7 9.6 - - - +
93G PRO* 3.2 26.5 + - - +
94G LYS* 3.3 15.0 + - - +
95G SER* 5.6 0.3 - - - -
119H VAL 3.1 13.0 - - - +
120H THR* 3.7 16.8 - - + +
122H PHE* 3.6 3.8 - - - -
147H LEU* 4.2 2.1 - - - +
148H ILE* 3.0 52.4 + - + +
150H ASN* 2.9 27.5 - - - +
155H PHE* 1.3 77.1 - - - +
157H VAL* 1.3 62.6 + - - +
158H LEU* 3.8 21.3 - - - +
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Residues in contact with VAL 157 (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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117H CYS 3.8 1.2 - - - +
119H VAL* 3.0 45.7 + - + +
122H PHE* 4.2 13.5 - - + -
127H ILE* 4.7 5.4 - - + -
129H VAL* 3.9 18.4 - - + -
144H SER* 4.4 8.1 - - - +
145H THR* 3.6 28.9 - - - +
146H GLN 4.3 5.4 - - - +
147H LEU* 5.0 5.8 - - + +
148H ILE* 4.9 0.4 - - - -
156H GLN* 1.3 76.8 - - - +
158H LEU* 1.3 69.8 - - - +
159H VAL* 4.4 3.1 - - + -
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Residues in contact with LEU 158 (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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116H VAL* 4.4 9.9 - - + -
117H CYS 3.7 2.2 - - - -
118H SER* 3.7 28.9 - - - +
119H VAL 4.7 0.7 - - - +
120H THR* 5.1 1.1 - - + -
144H SER* 3.0 3.6 - - - -
145H THR* 2.8 50.5 + - + +
148H ILE* 4.6 7.9 - - + -
156H GLN* 3.8 22.2 - - - +
157H VAL* 1.3 79.9 - - - +
159H VAL* 1.3 63.0 + - - +
160H MET* 3.9 11.6 - - - +
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Residues in contact with VAL 159 (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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116H VAL* 3.5 0.2 - - - -
117H CYS* 2.7 41.1 + - + +
129H VAL* 3.6 40.6 - - + +
130H ARG* 6.0 0.4 - - - -
131H TRP* 3.3 28.9 + - + +
142H VAL* 4.0 14.1 - - + -
143H SER 3.4 3.8 - - - +
144H SER* 3.4 25.1 - - - -
157H VAL* 4.4 8.5 - - + -
158H LEU* 1.3 80.0 - - - +
160H MET* 1.3 63.6 + - - +
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Residues in contact with MET 160 (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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114H THR* 3.7 15.3 - - + -
115H LEU 3.4 3.6 - - - -
116H VAL* 3.8 23.6 - - + -
131H TRP* 4.0 0.9 - - - -
141H GLY 4.1 1.1 - - - -
142H VAL* 3.2 9.7 - - - +
143H SER* 2.7 60.5 + - - +
144H SER 4.9 0.4 - - - -
145H THR* 4.4 17.0 - - + +
158H LEU* 3.9 22.7 - - - +
159H VAL* 1.3 80.3 - - - +
161H LEU* 1.3 60.7 + - - +
162H GLU* 4.3 6.5 - - - +
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Residues in contact with LEU 161 (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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114H THR* 3.5 1.0 - - - -
115H LEU* 3.0 35.1 + - + +
131H TRP* 3.7 42.2 - - + +
132H PHE 5.4 0.4 - - - +
138H GLU* 4.3 22.7 - - + +
141H GLY* 3.1 6.7 - - - +
142H VAL* 3.7 21.3 - - + -
160H MET* 1.3 77.2 - - - +
162H GLU* 1.3 78.0 + - - +
163H MET* 3.2 7.5 + - + +
171H TYR* 3.6 34.3 - - + -
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Residues in contact with GLU 162 (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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112H HIS* 4.7 18.6 + - + -
113H ASN 3.5 6.2 - - - +
114H THR* 2.8 31.5 + - - +
141H GLY* 2.7 34.6 + - - +
143H SER* 5.1 4.2 + - - -
160H MET* 4.3 9.0 - - - +
161H LEU* 1.3 78.5 - - - +
163H MET* 1.3 59.1 + - - +
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Residues in contact with MET 163 (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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103H LEU* 4.5 9.2 - - + -
111H HIS 3.1 1.7 - - - +
112H HIS* 3.7 4.9 + - - -
113H ASN 3.0 37.0 + - - +
115H LEU* 3.6 29.4 - - + +
138H GLU* 6.1 0.4 - - - +
161H LEU* 3.6 17.7 - - + +
162H GLU* 1.3 75.1 - - - +
164H THR* 1.3 63.7 + - - +
165H PRO* 3.3 45.1 - - + -
171H TYR* 3.7 37.2 - - + +
188H TRP* 3.9 13.9 - - + -
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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