Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 3U8M
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 ALA 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ASP 3.8 3.1 - - - +
125A VAL* 3.4 21.3 - - - +
126A SER 3.4 20.6 - - - +
127A GLY 3.5 1.8 + - - -
128A VAL* 3.6 11.1 - - + +
133A GLY* 1.3 74.2 - - - -
135A THR* 1.3 57.1 + - - +
136A CYS 4.0 0.9 - - - -
199A LEU 3.4 0.7 - - - +
200A ASN* 2.7 22.5 + - - -
201A PHE* 2.6 43.3 + - + -
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Residues in contact with THR 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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124A ASP* 3.3 25.4 + - - +
126A SER 4.6 1.2 + - - -
133A GLY 4.2 0.7 + - - -
134A ALA* 1.3 72.2 - - - +
136A CYS* 1.3 62.0 + - - +
137A ARG* 3.8 3.5 + - + +
198A SER* 4.1 27.1 - - - +
199A LEU 3.3 7.4 - - - +
200A ASN* 3.2 23.3 + - + +
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Residues in contact with CYS 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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48A VAL* 3.9 13.5 - - - -
121A PHE* 5.1 0.2 - - - -
123A CYS* 2.0 49.4 - - - -
124A ASP 4.0 4.3 - - - +
125A VAL* 6.0 0.2 - - + -
134A ALA 4.0 0.2 - - - -
135A THR* 1.3 71.6 - - - +
137A ARG* 1.3 59.5 + - - +
138A ILE* 3.5 19.2 + - - +
197A VAL 3.3 4.3 - - - +
198A SER* 4.5 0.9 - - - -
199A LEU* 2.7 49.9 + - + +
201A PHE* 4.0 17.3 - - + -
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Residues in contact with ARG 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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90A ASN* 2.8 23.0 + - - -
123A CYS* 3.9 7.0 - - + +
124A ASP* 5.0 0.6 - - - +
135A THR* 3.8 5.9 + - + +
136A CYS* 1.3 73.8 - - - +
138A ILE* 1.3 60.7 + - - +
139A LYS* 3.9 3.7 + - + +
196A GLU* 3.8 40.5 + - + +
197A VAL 3.6 3.4 - - - +
198A SER* 4.2 16.4 - - - +
167B GLN* 3.8 17.2 + - - +
168B TYR* 3.1 36.6 + - + -
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Residues in contact with ILE 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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33A LEU* 4.3 16.6 - - + -
35A PHE* 4.1 29.4 - - + -
50A VAL* 5.1 4.9 - - + -
52A PHE* 5.5 0.4 - - + -
88A ALA* 4.5 0.4 - - + -
90A ASN* 3.7 3.4 - - - +
121A PHE* 3.8 56.3 - - + -
136A CYS* 3.5 17.5 + - - +
137A ARG* 1.3 75.1 - - - +
139A LYS* 1.3 61.1 + - - +
140A ILE* 3.9 19.6 + - + +
195A VAL 3.6 2.1 - - - +
196A GLU* 3.5 2.0 - - - -
197A VAL* 2.8 44.7 + - - +
199A LEU* 5.5 1.8 - - + -
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Residues in contact with LYS 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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87A ALA 3.6 0.2 - - - +
88A ALA* 3.1 4.3 - - - -
89A TYR* 2.7 68.3 + - + -
90A ASN* 3.1 15.1 + - - +
137A ARG* 3.9 4.0 + - - +
138A ILE* 1.3 71.4 - - - +
140A ILE* 1.3 59.9 + - - +
183A VAL* 4.8 5.4 - - - +
185A TYR* 3.0 28.7 + - - -
194A ASP* 3.3 37.4 + - - +
195A VAL 3.6 3.6 - - - -
196A GLU* 4.1 20.2 - - + +
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Residues in contact with ILE 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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31A VAL* 4.4 20.5 - - + +
33A LEU* 3.8 40.2 - - + -
52A PHE* 5.2 2.7 - - + -
54A GLN* 3.9 17.5 - - - +
86A LEU* 4.1 22.7 - - + -
87A ALA 3.2 10.1 - - - +
88A ALA* 4.2 11.9 - - + -
89A TYR* 4.7 0.2 - - - -
138A ILE* 4.0 13.7 - - + +
139A LYS* 1.3 80.3 - - - +
141A GLY* 1.3 60.8 + - - +
152A VAL* 4.8 1.7 - - - +
194A ASP* 3.3 3.3 - - - -
195A VAL* 2.7 44.4 + - + +
197A VAL* 5.3 3.1 - - + -
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Residues in contact with GLY 141 (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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86A LEU* 3.2 10.0 - - - -
87A ALA* 2.8 31.6 + - - +
89A TYR* 4.0 8.9 - - - -
140A ILE* 1.3 77.3 - - - +
142A SER* 1.3 67.5 + - - -
143A TRP* 4.4 0.2 - - - -
152A VAL* 4.6 3.8 - - - -
193A GLU 3.6 16.2 - - - -
194A ASP* 4.0 3.8 - - - -
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Residues in contact with SER 142 (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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85A ASP* 2.7 28.5 + - - -
86A LEU* 3.7 8.5 - - - +
89A TYR* 3.5 15.0 + - - -
141A GLY* 1.3 73.8 - - - -
143A TRP* 1.3 61.4 + - - +
145A HIS* 3.0 38.3 + - - +
150A ILE* 4.0 23.6 - - - -
152A VAL* 4.6 2.0 - - - +
192A TYR* 4.6 5.9 - - - +
193A GLU 3.8 10.4 + - - +
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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