Contacts of the strand formed by residues 111 - 119 (chain A) in PDB entry 5H4Y
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 GLN 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY* 1.3 76.3 - - - +
112A LEU* 1.3 61.6 + - - +
132A ALA* 3.2 6.1 - - - +
133A MET* 2.8 52.7 + - + +
135A LEU* 4.6 0.4 - - - +
226A TRP* 3.3 44.5 - - + +
227A ARG 3.3 15.0 - - - +
228A GLU* 3.0 25.9 + - - +
229A LEU* 3.7 6.8 - - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 1.3 76.4 - - - +
113A GLN* 1.3 65.6 + - - +
114A TYR* 3.9 6.5 - - + -
129A ILE* 4.1 22.0 - - + -
131A GLN 3.4 17.7 - - - +
132A ALA* 4.0 12.8 - - + -
148A VAL* 4.3 12.1 - - + -
173A PHE* 4.2 6.3 - - + -
193A MET* 3.7 46.4 - - + -
195A VAL* 4.5 8.7 - - + -
210A VAL* 4.1 12.3 - - + -
225A ALA 3.7 0.9 - - - +
226A TRP* 3.3 5.8 - - - -
227A ARG 2.9 29.6 + - - -
229A LEU* 3.8 12.5 - - + +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 1.3 74.6 - - - +
114A TYR* 1.3 65.0 + - - +
130A LEU* 2.9 52.9 + - + +
131A GLN* 2.8 46.8 + - + +
224A GLN* 3.7 19.6 - - + +
225A ALA 3.3 11.9 - - - +
226A TRP* 3.3 43.0 + - + +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 3.9 14.4 - - + -
113A GLN* 1.3 75.6 - - - +
115A SER* 1.3 63.2 + - - +
116A LEU* 3.9 36.3 - - + -
128A GLY 3.1 14.4 - - - +
129A ILE* 4.6 2.0 - - + -
130A LEU* 4.2 5.8 - - - -
193A MET* 3.7 38.4 - - + -
210A VAL* 4.4 0.4 - - + -
212A VAL* 3.7 15.5 - - + +
223A VAL* 5.5 2.5 - - + -
224A GLN* 3.4 4.7 - - - +
225A ALA* 2.9 58.0 + - + +
227A ARG* 3.2 46.5 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 1.3 75.5 - - - +
116A LEU* 1.3 74.0 + - - +
117A ASP* 5.9 2.1 - - - +
126A LEU 5.1 0.5 + - - -
127A VAL* 3.5 1.6 - - - +
128A GLY* 2.9 45.6 + - - +
130A LEU* 3.8 12.7 - - - +
222A PRO* 6.5 0.4 - - - -
223A VAL 3.2 11.7 - - - -
224A GLN* 4.6 8.7 - - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.9 25.4 - - + -
115A SER* 1.3 83.7 - - - +
117A ASP* 1.3 59.8 + - - +
125A LEU* 4.4 5.6 - - + -
126A LEU 3.4 2.9 - - - +
127A VAL* 4.1 13.2 - - + -
191A LEU* 3.5 29.4 - - + -
212A VAL* 4.6 2.5 - - + -
214A MET* 4.2 11.4 - - + -
217A VAL* 3.8 36.3 - - + -
219A LEU* 3.6 15.3 - - + +
222A PRO* 3.2 5.0 - - - +
223A VAL* 2.8 44.8 + - + +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER* 5.7 2.9 - - - +
116A LEU* 1.3 75.3 - - - +
118A TYR* 1.3 74.3 + - - +
119A ASP* 3.6 3.6 + - - -
125A LEU* 4.3 2.8 - - - +
126A LEU* 2.7 59.4 + - + +
219A LEU* 4.8 0.2 - - - -
222A PRO* 3.5 31.5 - - + +
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 4.3 0.6 - - - -
117A ASP* 1.3 79.8 + - - +
119A ASP* 1.3 57.9 + - - +
120A PHE* 3.3 63.5 + + + -
123A GLY* 3.3 17.0 - - - -
124A GLN 3.5 20.9 - - - -
125A LEU* 3.9 9.5 - - + +
181A VAL* 2.6 31.3 + - + -
182A PRO* 3.5 1.4 - - - +
183A TYR* 3.0 37.9 + + + +
186A LEU* 3.9 20.4 - - + -
219A LEU* 4.0 30.9 + - + +
222A PRO* 5.5 0.6 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 3.6 5.0 + - - +
118A TYR* 1.3 69.0 - - - +
120A PHE* 1.3 57.8 + - - +
121A GLN* 3.1 22.2 + - - +
122A SER* 3.2 26.9 + - - +
123A GLY* 2.8 26.7 + - - -
124A GLN 2.9 17.7 + - - +
126A LEU* 4.2 17.5 - - + +
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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