Contacts of the strand formed by residues 120 - 128 (chain A) in PDB entry 1QSR
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLN* 4.0 0.3 - - - -
115A TYR* 2.9 54.6 + + + +
118A GLN* 3.3 36.3 - - + -
119A ARG* 1.3 79.3 - - - +
121A ALA* 1.3 63.0 + - - +
154A ILE* 3.8 5.3 - - - +
156A TYR* 3.1 24.5 - - + +
158A LEU* 5.5 1.3 - - + -
180A MET* 4.0 21.5 - - + -
184A LYS* 3.7 22.2 - - + -
185A TRP* 3.7 22.7 - - + -
188A TYR* 3.8 15.9 - + + -
189A ILE* 3.8 24.2 - - + -
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Residues in contact with ALA 121 (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 PHE* 5.0 1.6 - - + -
113A ARG 3.3 13.7 - - - +
114A GLN* 4.1 9.6 - - + -
120A PHE* 1.3 81.5 - - - +
122A GLU* 1.3 62.5 + - - +
123A VAL 4.0 0.3 + - - -
145A PHE* 5.0 4.3 - - + -
149A MET* 3.9 28.3 - - - -
154A ILE* 4.0 4.5 - - + -
156A TYR 2.9 6.3 + - - -
157A LEU* 3.2 11.5 - - + +
158A LEU* 2.8 25.1 + - - +
189A ILE* 4.9 1.1 - - - -
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Residues in contact with GLU 122 (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 PHE* 3.2 6.6 - - - +
113A ARG* 2.9 38.5 + - + +
115A TYR* 4.5 12.0 + - + -
121A ALA* 1.3 73.5 - - - +
123A VAL* 1.3 74.7 + - - +
124A ALA* 3.5 9.8 + - + +
158A LEU 3.1 15.3 - - - +
159A THR* 4.7 1.1 - - - -
160A TYR* 4.1 20.1 + - - +
189A ILE* 3.7 41.5 - - + +
190A LYS 5.0 1.2 + - - -
192A TYR* 5.7 2.1 - - - -
197A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 123 (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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110A ILE* 3.8 22.2 - - + -
111A CYS 4.0 2.7 - - - -
112A PHE* 4.4 2.0 - - - -
122A GLU* 1.3 77.7 - - - +
124A ALA* 1.3 62.1 + - - +
125A PHE 4.1 8.1 - - - +
126A LEU* 4.3 18.2 - - + -
142A MET* 5.3 2.9 - - + -
145A PHE* 4.0 28.7 - - + -
157A LEU* 4.6 13.9 - - + -
158A LEU 2.8 12.3 + - - +
159A THR* 2.8 40.9 + - - +
160A TYR 4.7 0.9 + - - -
169A PHE* 4.7 2.7 - - + -
174A PHE* 4.8 9.4 - - + -
401A ACO 3.9 3.4 - - + +
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Residues in contact with ALA 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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80A MET* 5.4 2.1 - - - +
88A LEU* 4.3 8.7 - - + -
94A HIS* 4.1 24.2 - - + +
111A CYS 2.8 16.4 + - - +
112A PHE* 4.8 0.7 - - - -
113A ARG* 6.1 0.2 - - + -
122A GLU* 3.5 14.5 + - + +
123A VAL* 1.3 73.5 - - - +
125A PHE* 1.3 88.8 + - + +
401A ACO 3.6 13.5 - - - +
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Residues in contact with PHE 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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73A PHE* 3.7 35.7 - + + -
77A LEU* 3.9 17.7 - - + -
80A MET* 3.8 31.2 - - + -
84A TYR* 4.1 10.5 - + - -
85A ILE* 3.7 34.8 - - + -
88A LEU* 3.9 36.8 - - + -
89A VAL* 4.3 2.0 - - + -
110A ILE* 3.3 5.5 - - - +
111A CYS* 2.8 43.4 + - + +
123A VAL* 4.5 1.6 - - - -
124A ALA* 1.3 94.1 - - + +
126A LEU* 1.3 62.7 + - - +
401A ACO 3.7 6.1 - - - -
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Residues in contact with LEU 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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73A PHE* 3.7 2.2 - - - -
77A LEU* 4.6 2.5 - - - +
109A GLY 3.4 4.0 - - - +
110A ILE* 3.3 28.7 - - + -
123A VAL* 4.3 6.5 - - + -
125A PHE* 1.3 77.7 - - - +
127A ALA* 1.3 72.0 + - - +
138A GLY 5.4 0.2 - - - +
141A LEU* 3.5 17.5 - - + -
142A MET* 3.8 12.6 - - + -
168A TYR* 3.4 36.1 - - + +
169A PHE* 3.8 19.5 - - + -
401A ACO 2.7 60.7 + - + +
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Residues in contact with ALA 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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72A ILE* 4.3 7.0 - - + +
73A PHE* 3.7 18.9 - - + -
76A GLN* 3.8 23.8 - - + -
77A LEU* 5.3 1.3 - - + -
108A GLY* 3.1 2.7 - - - -
109A GLY 2.9 34.0 + - - +
126A LEU* 1.3 80.7 - - - +
128A VAL* 1.3 66.4 + - - +
141A LEU* 4.6 0.2 - - - +
401A ACO 3.2 19.3 - - + +
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Residues in contact with VAL 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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72A ILE* 4.2 2.9 - - - -
76A GLN* 3.7 5.0 - - - +
99A ILE* 4.3 12.6 - - + -
107A ILE 3.5 12.6 - - - +
127A ALA* 1.3 79.9 - - - +
129A THR* 1.3 74.3 + - - +
130A ALA 3.4 0.3 + - - -
132A GLU* 3.6 29.8 - - + +
133A GLN* 2.8 22.2 + - + +
137A TYR* 4.5 7.6 - - + -
138A GLY* 3.9 14.4 - - - +
141A LEU* 5.1 2.0 - - + -
401A ACO 2.7 46.1 + - + +
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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