Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 1MDL
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 VAL 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.6 15.3 - - + +
133A PRO* 1.3 78.0 - - - +
135A GLN* 1.4 70.9 + - - +
136A ALA* 4.3 0.2 - - - +
304A ALA* 4.0 26.2 - - + +
307A LEU* 4.1 31.6 - - + -
308A ALA* 4.8 4.5 - - - +
313A ALA* 5.3 6.5 - - + -
314A HIS 4.7 9.4 - - - +
316A LEU* 4.5 6.7 - - + +
336A ASN* 3.7 2.5 - - - -
337A ALA* 2.8 40.6 + - + +
339A ILE* 5.5 0.7 - - + -
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Residues in contact with GLN 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 PRO 4.3 1.0 + - - -
134A VAL* 1.4 72.0 - - - +
136A ALA* 1.4 58.5 + - - +
314A HIS* 3.1 31.8 - - - +
315A TRP* 3.4 45.7 + - + -
316A LEU* 2.9 22.2 + - - +
335A GLY 4.7 0.7 - - - +
336A ASN* 3.1 22.3 - - - +
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Residues in contact with ALA 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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134A VAL 4.3 4.0 - - - +
135A GLN* 1.4 75.7 - - - +
137A TYR* 1.3 61.1 + - - +
160A PHE* 3.6 14.3 - - + -
161A ARG 4.7 5.0 + - - -
162A ALA 4.5 0.7 - - - +
315A TRP* 3.5 11.4 - - - -
316A LEU* 3.0 20.4 - - + +
318A ARG* 4.7 0.4 - - + -
332A PHE* 3.8 31.2 - - + -
335A GLY 3.0 20.5 + - - +
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Residues in contact with TYR 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 ALA* 1.3 74.9 - - - +
138A ASP* 1.3 60.3 + - - +
139A SER* 4.1 3.1 - - - -
160A PHE* 4.4 1.3 - - - -
162A ALA* 3.2 31.9 - - + +
163A VAL 4.3 0.9 - - - +
164A LYS* 2.9 59.1 + - + -
193A MET* 4.0 10.5 - - + -
219A TRP* 3.8 26.6 - + - -
268A MET* 4.1 6.2 - - - +
295A SER* 5.5 0.7 - - - -
296A SER 4.3 2.2 + - - -
315A TRP* 3.8 21.5 - - + -
316A LEU 2.9 12.8 + - - -
317A GLU* 3.4 40.2 - - + +
318A ARG* 2.7 32.3 + - - +
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Residues in contact with ASP 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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20A TYR* 3.5 18.4 + - - -
137A TYR* 1.3 70.5 - - - +
139A SER* 1.3 64.5 + - - +
140A HIS* 2.7 32.9 + - + +
155A ALA* 3.8 22.9 - - + +
158A LEU* 5.7 1.2 - - - +
160A PHE* 4.2 13.1 - - + -
162A ALA 3.2 7.7 + - - +
163A VAL* 3.3 5.9 - - + +
164A LYS 3.0 23.0 + - - -
318A ARG* 3.1 39.9 + - - +
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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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20A TYR* 4.9 3.3 - - - +
137A TYR* 3.7 3.5 + - - -
138A ASP* 1.3 75.7 + - - +
140A HIS* 1.3 70.8 + - - +
151A ARG* 4.2 3.6 + - - -
164A LYS* 3.8 20.4 - - - +
317A GLU* 2.7 34.1 + - - -
318A ARG 3.0 21.3 + - - +
319A LEU* 4.3 19.7 - - - +
399A SMN 3.9 3.1 + - - -
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Residues in contact with HIS 140 (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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20A TYR* 3.7 10.0 - + - -
138A ASP* 2.7 29.9 + - - -
139A SER* 1.3 87.1 + - - +
141A SER* 1.3 62.9 + - - +
143A ASP* 3.5 13.2 - - - +
148A ALA* 4.8 3.7 + - + -
151A ARG* 3.2 64.9 - - + +
152A ALA* 4.3 2.0 + - - -
155A ALA* 4.2 0.4 - - + -
163A VAL* 3.9 28.1 - - + +
164A LYS* 2.9 21.3 + - - +
165A THR* 4.9 4.9 - - - -
166A ARG* 4.0 12.2 + - - +
319A LEU* 5.8 1.2 - - - +
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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