Contacts of the strand formed by residues 122 - 130 (chain A) in PDB entry 1Q4U
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 THR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLN* 4.2 13.8 + - - +
117A HIS* 3.6 14.7 - - + -
119A GLY* 2.8 32.5 + - - -
120A SER 3.8 0.4 - - - -
121A THR* 1.3 91.5 + - - +
123A TRP* 1.3 69.8 + - - +
124A PHE* 4.7 4.7 - - + +
143A SER* 3.4 25.4 - - - +
144A ILE 3.2 7.9 - - - +
146A VAL 4.6 0.2 - - - +
147A ARG* 5.1 0.7 + - - -
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Residues in contact with TRP 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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43A PRO 4.1 5.6 - - - -
79A ALA 4.5 0.2 - - - -
80A THR* 3.7 38.8 - - + +
83A VAL* 3.7 32.5 - - + -
84A VAL* 3.8 20.9 - - + +
115A ARG* 3.5 42.6 - - - -
117A HIS 3.2 4.7 - - - +
118A ALA* 3.7 19.0 - - + +
119A GLY 3.4 17.8 + - - -
122A THR* 1.3 85.0 - - - +
124A PHE* 1.3 62.5 + - - +
125A TRP* 3.9 15.3 - + + +
142A MET 3.8 0.3 - - - +
143A SER* 3.7 1.6 - - - -
144A ILE* 2.8 35.8 + - + +
146A VAL* 3.9 14.8 - - + +
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Residues in contact with PHE 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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115A ARG* 3.7 2.4 - - - +
116A ILE* 2.8 54.1 + - + +
117A HIS* 2.7 33.1 + - + +
122A THR* 5.1 3.1 - - + -
123A TRP* 1.3 75.4 - - - +
125A TRP* 1.3 63.2 + - - +
126A ASP* 3.7 18.2 - - - -
141A SER* 3.6 31.0 - - - -
142A MET 3.4 4.3 - - - -
143A SER* 3.9 30.1 - - - -
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Residues in contact with TRP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR 4.2 1.6 - - - -
43A PRO 3.5 23.6 - - - -
44A GLU 3.8 9.2 - - - -
45A ARG* 3.9 3.8 - - - -
76A ALA* 3.7 32.5 - - + -
79A ALA* 3.6 29.6 - - + -
80A THR* 3.0 20.5 + - - -
113A ALA* 3.6 26.0 - - + -
114A VAL 3.4 8.3 - - - -
115A ARG* 3.3 35.4 - - + +
123A TRP* 3.9 29.3 - + - +
124A PHE* 1.3 83.3 - - - +
126A ASP* 1.3 62.9 + - - +
127A VAL* 4.5 5.8 - - + -
140A SER 3.7 1.6 - - - +
141A SER* 3.8 2.1 - - - -
142A MET* 2.9 33.9 + - + +
144A ILE* 4.0 11.4 - - + -
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Residues in contact with ASP 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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112A GLU 3.4 3.1 - - - +
113A ALA* 3.4 0.2 - - - -
114A VAL* 2.9 40.9 + - + +
116A ILE* 3.7 35.5 - - + +
124A PHE* 3.7 12.3 - - - -
125A TRP* 1.3 72.5 - - - +
127A VAL* 1.3 60.5 + - - +
140A SER 3.9 2.6 - - - +
141A SER* 4.1 8.3 + - - -
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Residues in contact with VAL 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 ALA* 4.0 31.4 - - + +
75A LEU* 4.7 1.8 - - + -
76A ALA* 4.6 0.4 - - + -
111A ALA* 4.2 12.3 - - + -
112A GLU 3.2 14.8 - - - +
113A ALA* 3.9 17.3 - - + +
125A TRP* 4.3 6.7 - - + +
126A ASP* 1.3 77.5 - - - +
128A SER* 1.3 67.6 + - - +
129A LEU* 4.0 6.0 - - + +
139A VAL* 3.1 8.6 - - - +
140A SER* 2.7 43.9 + - - +
142A MET* 4.0 20.9 - - + -
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Residues in contact with SER 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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110A ARG 3.5 1.7 - - - +
111A ALA* 3.2 4.7 - - - +
112A GLU* 2.9 49.2 + - - +
126A ASP 4.1 0.4 + - - -
127A VAL* 1.3 73.0 - - - +
129A LEU* 1.3 61.1 + - - +
130A ARG* 4.1 20.0 + - - +
136A LEU* 3.6 20.6 - - - -
138A ALA 3.8 3.4 - - - -
139A VAL* 4.4 4.3 - - - -
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Residues in contact with LEU 129 (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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68A TYR* 3.8 46.0 - - + +
71A LEU* 4.0 17.0 - - + -
72A ALA* 4.6 2.7 - - + +
98A THR* 5.1 0.7 - - + -
109A VAL* 4.1 10.8 - - + -
110A ARG 3.3 2.9 - - - -
111A ALA* 4.0 20.2 - - + -
127A VAL* 4.0 17.0 - - + +
128A SER* 1.3 80.1 - - - +
130A ARG* 1.3 62.1 + - - +
136A LEU* 3.8 1.2 - - - +
137A CYS* 2.9 26.6 + - - -
138A ALA* 2.8 36.3 + - + +
139A VAL* 4.2 7.0 - - - -
140A SER* 4.3 7.4 - - - +
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Residues in contact with ARG 130 (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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104A VAL* 5.5 0.9 - - - -
109A VAL* 3.5 8.2 - - - +
110A ARG* 2.7 50.0 + - + +
112A GLU* 5.6 2.4 + - - -
128A SER* 4.1 16.5 + - - +
129A LEU* 1.3 79.7 - - - +
131A ASP* 1.3 69.5 + - - +
134A GLY* 2.9 34.9 + - - +
135A ARG 3.0 11.0 - - - +
136A LEU* 3.6 36.0 - - + +
137A CYS* 4.4 4.0 - - - +
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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