Contacts of the strand formed by residues 137 - 148 (chain A) in PDB entry 2A34
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 CYS 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 4.3 12.1 - - + -
58A ARG 3.3 16.8 - - - +
59A TYR* 3.5 19.7 - - + -
125A THR* 3.7 5.9 - - - +
126A LEU* 2.9 40.7 + - - +
135A LYS 3.9 11.2 - - - -
136A PRO* 1.3 77.0 - - - +
138A GLY* 1.3 60.0 + - - +
238A VAL* 5.2 11.2 - - - -
314A ILE* 4.0 23.1 - - - -
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Residues in contact with GLY 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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56A ALA 3.9 0.2 - - - +
57A PHE* 3.5 8.0 - - - -
58A ARG* 2.9 34.4 + - - +
124A VAL* 3.1 15.0 - - - -
125A THR* 4.4 1.1 - - - -
137A CYS* 1.3 79.5 - - - +
139A ILE* 1.3 65.2 + - - -
140A ASP* 4.2 5.6 - - - -
314A ILE* 4.6 8.3 - - - -
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Residues in contact with ILE 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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55A CYS* 3.8 25.4 - - - -
56A ALA 3.4 3.1 - - - +
57A PHE* 3.7 29.2 - - + -
75A LEU* 3.7 16.4 - - + -
121A PRO* 3.6 30.7 - - + +
122A CYS 3.7 20.4 - - - +
123A SER* 3.2 20.5 + - - -
124A VAL* 3.0 26.7 + - + +
138A GLY* 1.3 76.8 - - - -
140A ASP* 1.3 70.1 + - - +
141A PHE* 4.8 1.6 - - + -
311A LEU 5.1 2.0 - - - +
312A LEU 4.5 7.4 - - - +
313A GLY* 5.5 0.2 - - - -
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Residues in contact with ASP 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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54A THR 3.5 2.1 - - - +
55A CYS* 3.6 3.1 - - - -
56A ALA 3.1 30.0 + - - -
58A ARG* 3.3 39.7 + - - +
123A SER* 4.2 7.6 + - - -
124A VAL 5.6 0.2 - - - -
125A THR* 4.8 9.4 + - - -
138A GLY* 4.3 4.4 + - - -
139A ILE* 1.3 82.6 - - - +
141A PHE* 1.3 64.9 + - - +
142A GLU* 6.1 0.4 - - + -
164A VAL* 3.9 24.5 - - + +
165A VAL 5.3 0.4 - - - +
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Residues in contact with PHE 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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53A LEU* 4.8 7.4 - - + -
54A THR 3.3 5.4 - - - +
55A CYS* 3.7 36.3 - - + -
116A MET* 3.5 25.4 - - + -
120A LEU* 5.2 5.8 - - + -
121A PRO 3.4 22.0 - - - -
122A CYS 4.5 0.2 - - - -
123A SER* 3.6 23.3 - - - -
139A ILE* 4.8 1.1 - - + -
140A ASP* 1.3 74.4 - - - +
142A GLU* 1.3 61.2 + - - +
164A VAL* 3.4 7.8 - - - +
165A VAL* 3.0 48.3 + - + +
166A ARG 4.3 0.4 - - - -
167A LYS* 3.2 50.3 - - + -
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Residues in contact with GLU 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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52A MET 3.4 5.0 - - - +
53A LEU* 3.5 3.1 - - - +
54A THR* 3.1 44.2 + - - +
58A ARG* 3.9 22.7 + - - +
72A ARG* 5.2 4.0 + - - -
140A ASP* 6.1 0.4 - - + -
141A PHE* 1.3 76.0 - - - +
143A VAL* 1.3 70.9 + - - +
144A LYS* 3.2 39.2 + - - +
162A ARG* 3.7 25.3 + - + +
163A LEU 3.2 10.5 - - - +
164A VAL* 5.2 5.3 - - + +
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Residues in contact with VAL 143 (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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16A ILE* 5.0 12.9 - - + +
18A LEU* 5.3 2.0 - - + -
33A ILE* 4.3 19.3 - - + -
51A VAL* 4.1 12.6 - - + -
52A MET 3.5 4.3 - - - +
53A LEU* 3.9 19.7 - - + -
112A PHE* 3.9 30.3 - - + -
114A LEU* 5.0 2.7 - - + -
142A GLU* 1.3 75.1 - - - +
144A LYS* 1.3 61.7 + - - +
145A SER* 5.2 1.8 - - - +
161A VAL 3.4 1.7 - - - +
162A ARG* 3.4 2.1 - - - -
163A LEU* 2.9 47.7 + - + +
165A VAL* 4.8 11.9 - - + -
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Residues in contact with LYS 144 (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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51A VAL* 3.7 2.6 - - - -
52A MET* 3.1 47.1 + - + +
54A THR* 6.2 0.8 - - - +
142A GLU* 3.2 28.3 + - + +
143A VAL* 1.3 73.4 - - - +
145A SER* 1.3 61.3 + - - +
146A PHE* 3.7 34.5 - - + -
155A VAL* 4.7 16.0 - - + +
160A TYR* 3.9 28.3 - - + -
161A VAL 3.0 13.0 - - - +
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Residues in contact with SER 145 (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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14A LEU* 4.3 6.1 - - - +
16A ILE* 4.5 2.0 - - - -
37A VAL* 3.7 20.2 - - - +
49A LEU* 3.3 27.2 - - - +
50A PHE 3.2 15.5 + - - -
51A VAL* 3.7 7.4 - - - +
112A PHE* 6.2 0.2 - - - -
143A VAL* 4.2 3.2 - - - +
144A LYS* 1.3 72.4 - - - +
146A PHE* 1.3 61.1 + - - +
159A ASP 4.0 0.3 - - - +
160A TYR* 3.2 4.5 - - - +
161A VAL* 3.0 43.7 + - - +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LYS 3.9 0.2 - - - +
49A LEU* 3.7 7.6 - - - +
50A PHE* 3.2 51.4 + + + -
52A MET* 4.5 25.1 - - + -
79A THR* 5.2 2.0 - - + -
144A LYS* 3.7 37.9 - - - -
145A SER* 1.3 76.3 + - - +
147A CYS* 1.3 60.6 + - - +
148A ALA* 3.7 26.7 + - + -
150A ASN 5.2 2.5 - - - -
151A PRO* 5.4 9.6 - - + -
153A GLU 5.6 1.3 - - - -
155A VAL* 3.5 44.4 - - + -
159A ASP 3.3 9.9 - - - +
160A TYR* 4.0 3.1 - - + -
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Residues in contact with CYS 147 (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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14A LEU* 3.7 22.0 - - - -
43A TYR* 4.9 4.3 - - - -
44A LEU* 3.4 44.9 - - + -
47A ARG* 3.7 18.0 + - + +
48A LYS 3.7 7.2 - - - -
49A LEU* 4.4 1.6 - - - -
146A PHE* 1.3 74.2 - - - +
148A ALA* 1.3 62.7 + - - +
155A VAL* 5.6 1.7 - - - +
156A SER 5.5 3.1 + - - -
159A ASP* 3.2 39.0 + - - +
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Residues in contact with ALA 148 (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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47A ARG* 3.7 15.5 - - - +
48A LYS* 3.3 28.6 + - - +
50A PHE* 3.6 11.5 - - + -
146A PHE* 3.7 24.1 + - + -
147A CYS* 1.3 75.2 - - - +
149A GLU* 1.3 62.6 + - - +
150A ASN 3.4 19.1 - - - +
153A GLU* 4.3 11.7 - - + +
154A THR 5.5 2.9 - - - +
155A VAL* 5.7 1.3 - - + -
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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