Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 1MAQ
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 ARG 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU 3.4 15.0 + - - -
120A GLN* 2.8 40.0 + - - +
123A PHE* 2.5 32.3 + - - +
124A LYS* 4.8 0.8 - - - +
126A SER* 1.3 90.3 + - - +
130A ASP* 1.3 58.6 + - - +
151A GLY 4.6 7.2 + - - +
152A LEU* 3.4 26.7 - - + +
154A GLN* 2.5 48.6 + - + +
185A ILE* 5.1 1.1 - - - -
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Residues in contact with ASP 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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126A SER* 3.3 12.4 + - - +
129A ARG* 1.3 80.9 + - - +
133A VAL* 1.3 61.6 + - - +
134A TYR* 4.0 13.9 + - + -
154A GLN* 3.1 28.3 - - - +
156A GLN* 3.5 32.4 - - + +
181A PRO* 5.7 4.3 - - - +
184A SER* 5.0 2.7 + - - -
185A ILE* 3.2 31.9 + - - +
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Residues in contact with VAL 133 (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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130A ASP* 1.3 75.0 - - - +
134A TYR* 1.3 65.8 + - - +
135A LEU* 3.6 20.0 + - + -
147A PHE* 3.8 41.7 - - + -
152A LEU* 4.1 16.8 - - + -
154A GLN 2.9 9.6 + - - +
155A LEU* 3.6 8.6 - - + +
156A GLN 2.9 22.1 + - - +
185A ILE* 3.4 33.4 - - + +
187A LEU* 4.5 10.1 - - + -
220A TYR* 5.8 0.7 - - + -
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Residues in contact with TYR 134 (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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130A ASP* 4.0 15.7 + - + -
133A VAL* 1.3 76.0 - - - +
135A LEU* 1.3 60.6 + - - +
156A GLN* 3.4 40.7 + - + +
157A ALA 3.9 20.4 - - - -
158A TYR* 3.5 18.2 - - + -
180A ILE* 3.5 47.5 - - + -
181A PRO* 3.5 19.5 - - + +
184A SER* 4.0 8.1 - - - -
185A ILE 2.8 21.1 + - - +
186A ILE* 4.1 8.3 - - + -
187A LEU* 3.0 24.1 + - - +
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Residues in contact with LEU 135 (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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133A VAL* 4.1 18.8 - - + -
134A TYR* 1.3 77.4 - - - +
136A PRO* 1.3 77.7 - - + +
139A SER* 4.4 7.0 - - - -
143A HIS* 3.9 22.2 - - + -
144A THR* 3.6 24.7 - - - +
147A PHE* 4.2 14.4 - - + -
155A LEU* 3.9 21.8 - - + -
156A GLN 3.0 14.2 + - - +
157A ALA* 3.2 7.2 - - + +
158A TYR* 3.1 22.0 + - - -
187A LEU* 4.2 14.4 - - + -
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Residues in contact with PRO 136 (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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135A LEU* 1.3 95.1 - - + +
137A LYS* 1.3 60.7 + - - +
138A PRO* 3.2 19.7 - - - +
139A SER* 3.4 17.4 + - - +
157A ALA* 5.4 0.2 - - - +
158A TYR* 3.5 32.5 - - + +
160A TYR* 3.9 13.2 - - + -
187A LEU* 3.8 17.5 - - + +
189A HIS* 3.9 14.6 - - + -
193A HIS* 3.7 22.4 - - + +
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Residues in contact with LYS 137 (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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136A PRO* 1.3 74.8 - - - +
138A PRO* 1.3 62.6 - - + +
157A ALA* 3.6 31.0 - - + +
158A TYR 3.1 23.8 + - - +
159A ARG* 4.6 9.8 - - + +
160A TYR* 3.2 6.1 + - - +
161A TYR* 2.9 28.1 + - - +
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Residues in contact with PRO 138 (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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136A PRO 3.2 13.4 - - - +
137A LYS* 1.3 81.6 - - + +
139A SER* 1.3 63.0 + - - +
161A TYR* 3.6 22.0 - - + -
193A HIS* 3.1 25.3 + - + -
195A PRO* 4.2 10.1 - - + -
196A THR* 3.7 19.3 - - + -
362A PHE* 4.2 17.5 - - + -
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Residues in contact with SER 139 (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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135A LEU* 4.4 11.9 - - - -
136A PRO* 3.4 24.7 + - - +
138A PRO* 1.3 78.2 - - - +
140A TRP* 1.3 66.1 + - - +
141A GLY* 3.1 4.2 + - - -
143A HIS* 2.8 28.7 + - - +
189A HIS* 3.1 14.0 + - - -
194A ASN 3.8 10.3 - - - -
195A PRO* 4.2 6.4 - - - +
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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