Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 1QHP
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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 3.5 42.0 + - - +
3A SER* 3.8 14.8 - - - +
5A SER 4.5 1.2 + - - -
6A VAL* 4.1 13.0 - - - -
9A ASP* 2.7 36.4 + - - -
67A THR* 2.8 13.7 + - - -
68A THR* 3.4 14.5 + - + +
69A ILE 2.8 28.3 + - - -
118A HIS* 4.2 4.0 - - + -
121A GLY 5.5 3.6 + - - +
122A ILE* 1.3 82.0 - - - +
124A VAL* 1.3 59.6 + - - +
223A ASP* 3.3 25.8 - - + +
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Residues in contact with VAL 124 (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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69A ILE* 3.4 14.1 - - + +
71A LEU* 3.6 35.0 - - + -
110A PHE* 5.2 0.2 - - + -
113A LEU* 5.1 5.6 - - + +
114A VAL* 4.2 31.6 - - + -
117A ALA* 3.8 24.2 - - + -
118A HIS* 5.3 0.4 - - - +
123A LYS* 1.3 80.0 - - - +
125A ILE* 1.3 67.0 + - - +
126A VAL* 4.3 6.7 - - + -
222A ALA* 3.7 3.3 - - - -
223A ASP* 2.8 43.2 + - - +
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Residues in contact with ILE 125 (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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6A VAL* 5.8 2.0 - - + -
11A ILE* 4.8 13.0 - - + -
68A THR* 4.0 20.0 - - + -
69A ILE 2.8 9.2 + - - +
70A TRP* 3.5 29.1 - - + -
71A LEU* 3.0 26.5 + - - +
123A LYS* 4.3 0.4 - - + -
124A VAL* 1.3 77.6 - - - +
126A VAL* 1.3 64.5 + - - +
223A ASP* 4.0 7.4 - - + +
224A GLY* 3.3 30.5 - - - +
225A LEU* 4.0 2.7 - - - +
226A ARG* 4.5 18.6 - - + +
252A PHE* 4.7 15.3 - - + +
254A VAL* 4.5 14.1 - - + -
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Residues in contact with VAL 126 (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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70A TRP* 5.0 0.2 - - - -
71A LEU* 3.9 6.1 - - + +
74A VAL* 4.0 30.7 - - + +
75A LEU* 6.1 0.7 - - + -
110A PHE* 4.0 29.2 - - + -
124A VAL* 4.3 7.9 - - + -
125A ILE* 1.3 78.4 - - - +
127A ASP* 1.3 75.7 + - - +
128A PHE 3.3 2.1 + - - -
217A LEU* 4.0 16.4 - - + -
222A ALA* 4.2 14.8 - - + -
224A GLY 3.0 7.5 + - - -
225A LEU* 3.2 18.6 - - + +
226A ARG* 2.9 20.2 + - - -
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Residues in contact with ASP 127 (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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13A GLN* 5.2 0.3 + - - -
70A TRP* 3.0 19.3 + - - +
71A LEU 2.9 21.4 + - - +
72A SER* 3.8 1.3 - - - -
73A PRO* 3.3 37.9 - - + +
74A VAL 4.5 0.3 + - - -
75A LEU* 6.1 1.0 - - - +
92A TYR* 2.6 32.2 + - - -
126A VAL* 1.3 76.9 - - - +
128A PHE* 1.3 61.0 + - - +
226A ARG* 2.9 41.6 + - - +
228A ASP* 3.9 3.8 - - - +
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Residues in contact with PHE 128 (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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75A LEU* 4.1 11.4 - - + -
97A PHE* 3.9 24.7 - + - -
126A VAL 4.1 7.4 - - - +
127A ASP* 1.3 73.6 + - - +
129A VAL* 1.3 60.0 + - - +
130A PRO* 3.1 31.9 - - + +
210A LEU* 3.4 29.4 - - + -
213A ALA* 4.1 9.4 - - + -
214A ALA* 3.8 24.7 - - + -
217A LEU* 3.9 17.5 - - + -
225A LEU* 4.2 24.0 - - + -
226A ARG 2.9 9.4 + - - +
227A ILE* 3.7 5.3 - - + -
228A ASP* 2.8 28.4 + - - +
241A LEU* 4.4 12.3 - - + -
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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