Contacts of the strand formed by residues 122 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B GLN* 4.7 11.7 + - - +
117B HIS* 3.3 15.7 - - + -
119B GLY* 2.6 32.7 + - - -
120B SER 3.7 0.6 - - - -
121B THR* 1.3 91.8 + - - +
123B TRP* 1.3 70.2 + - - +
124B PHE* 4.7 4.3 - - + +
143B SER* 3.6 24.0 - - - +
144B ILE 3.3 9.8 + - - +
147B ARG* 5.1 0.9 + - - -
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO 4.0 3.1 - - - -
80B THR* 3.7 38.8 - - + +
83B VAL* 3.7 31.6 - - + -
84B VAL* 3.9 18.0 - - + +
115B ARG* 3.5 38.8 - - - -
117B HIS 3.2 4.7 - - - +
118B ALA* 3.6 22.0 - - + +
119B GLY 3.3 25.6 + - - -
122B THR* 1.3 77.5 - - - +
124B PHE* 1.3 61.7 + - - +
125B TRP* 3.7 22.7 - + - +
143B SER* 3.7 1.4 - - - -
144B ILE* 2.8 38.3 + - + +
146B VAL* 3.9 15.3 - - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ARG* 3.6 3.3 - - - +
116B ILE* 2.7 54.8 + - + -
117B HIS* 2.8 32.8 + - + +
122B THR* 5.2 2.9 - - + -
123B TRP* 1.3 75.4 - - - +
125B TRP* 1.3 65.0 + - - +
126B ASP* 3.8 18.2 - - - -
141B SER* 3.6 31.0 - - - -
142B MET 3.4 7.2 - - - -
143B SER* 4.0 24.9 - - - -
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR 4.2 0.9 - - - -
43B PRO 3.3 28.7 - - - -
44B GLU 3.7 9.4 - - - -
45B ARG* 3.8 3.4 - - - -
46B ALA 4.3 1.1 - - - -
76B ALA* 3.6 25.8 + - + -
79B ALA* 3.7 29.2 - - + -
80B THR* 2.9 22.6 + - - -
113B ALA* 3.7 25.1 - - + -
114B VAL 3.4 6.5 - - - -
115B ARG* 3.1 35.9 - - + +
123B TRP* 3.7 24.4 - + - +
124B PHE* 1.3 86.3 - - - +
126B ASP* 1.3 59.9 + - - +
127B VAL* 3.8 5.8 + - + -
140B SER 3.6 1.2 - - - +
141B SER* 3.7 2.1 - - - -
142B MET* 2.9 37.4 + - + +
144B ILE* 3.9 18.6 - - + -
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU 3.5 2.1 - - - +
113B ALA* 3.4 0.3 - - - -
114B VAL* 2.8 41.9 + - + +
116B ILE* 3.6 35.2 - - + +
124B PHE* 3.8 11.4 - - - -
125B TRP* 1.3 71.4 - - - +
127B VAL* 1.3 61.2 - - - +
128B SER* 4.1 2.8 + - - +
140B SER 3.8 3.4 - - - -
141B SER* 4.2 7.6 + - - -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 4.0 27.8 - - + +
75B LEU* 4.7 1.6 - - + -
76B ALA* 4.5 3.4 - - + -
111B ALA* 4.0 20.6 - - + -
112B GLU 3.1 14.1 - - - +
113B ALA* 3.8 18.6 - - + +
125B TRP* 4.4 2.9 - - + +
126B ASP* 1.3 76.0 - - - +
128B SER* 1.3 64.6 + - - +
129B LEU* 4.1 3.5 - - + +
139B VAL* 3.3 9.5 - - - +
140B SER* 2.7 43.6 + - - +
142B MET* 3.9 22.4 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ARG 3.4 1.9 - - - +
111B ALA* 3.1 5.7 - - - -
112B GLU* 2.7 49.4 + - - +
126B ASP* 4.1 1.9 + - - +
127B VAL* 1.3 74.6 + - - +
129B LEU* 1.3 60.6 + - - +
130B ARG* 4.1 17.5 + - - +
136B LEU* 3.8 19.7 - - - +
138B ALA 4.0 3.4 - - - -
139B VAL* 4.5 5.1 - - - +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.8 47.3 - - + +
71B LEU* 4.0 17.0 - - + -
72B ALA* 4.7 2.2 - - + +
98B THR* 5.1 0.9 - - + -
109B VAL* 4.1 11.2 - - + -
110B ARG 3.4 2.5 - - - -
111B ALA* 4.0 19.3 - - + -
127B VAL* 4.1 15.7 - - + +
128B SER* 1.3 78.5 - - - +
130B ARG* 1.3 55.3 + - - +
136B LEU* 3.7 1.4 - - - +
137B CYS* 2.7 34.4 + - - -
138B ALA* 2.8 36.0 + - + +
139B VAL* 4.1 8.1 - - - +
140B SER* 4.3 7.4 - - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 5.6 0.7 - - - -
109B VAL* 3.6 7.3 - - - +
110B ARG* 2.8 43.2 + - + +
112B GLU* 6.0 2.5 + - - +
128B SER* 4.4 15.1 + - - -
129B LEU* 1.3 80.0 - - - +
131B ASP* 1.3 67.1 + - - +
134B GLY* 3.0 29.0 + - - -
135B ARG 3.1 11.0 - - - +
136B LEU* 3.6 38.7 - - + +
137B CYS* 4.3 3.4 - - - +
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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