Contacts of the strand formed by residues 137 - 148 (chain A) in PDB entry 2O5J
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.9 1.0 - - - +
68A ILE* 4.1 19.4 - - - +
69A PRO 4.7 3.8 + - - -
71A VAL* 5.2 0.8 - - - +
103A ALA 4.4 1.1 - - - -
104A GLU* 4.5 16.5 - - + +
132A LEU* 4.1 0.6 - - - +
135A GLY 3.3 8.7 + - - +
136A GLY* 1.3 71.7 - - - +
138A LEU* 1.3 60.6 - - - +
139A ASN* 4.1 2.5 + - + -
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Residues in contact with LEU 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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58A ILE* 5.5 9.9 - - + -
68A ILE* 5.9 2.9 - - + -
71A VAL* 5.0 9.0 - - + -
78A ILE* 5.6 7.9 - - + -
101A LEU* 4.3 6.5 - - + -
102A LYS* 3.2 2.0 - - - +
103A ALA 3.0 38.7 + - - +
104A GLU* 4.6 2.1 + - - +
109A VAL* 4.1 26.7 - - + -
129A ILE* 5.1 1.6 - - + -
130A ALA* 4.7 20.6 - - + -
132A LEU* 3.8 19.3 - - + -
136A GLY 3.8 0.2 + - - -
137A ARG* 1.3 73.3 - - - +
139A ASN* 1.3 58.8 + - - +
140A MET* 3.5 37.0 - - + -
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Residues in contact with ASN 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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57A TYR* 3.8 0.9 - - - +
58A ILE* 3.9 4.6 - - - +
59A GLU* 3.0 58.3 + - + +
100A LEU* 4.1 4.7 - - - +
101A LEU 3.7 1.8 - - - -
102A LYS* 2.7 57.6 + - - +
104A GLU* 5.3 3.2 + - - +
137A ARG* 4.1 2.8 + - + -
138A LEU* 1.3 72.2 - - - +
140A MET* 1.3 61.3 + - - +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.6 2.7 - - + -
57A TYR 3.1 12.8 - - - +
58A ILE* 3.6 22.9 - - + -
78A ILE* 4.3 15.5 - - + -
82A LEU* 4.9 7.4 - - + -
100A LEU* 3.0 22.9 - - - +
101A LEU* 3.0 53.0 + - + +
114A PHE* 5.0 1.8 - - + -
129A ILE* 3.8 26.7 - - + -
138A LEU* 3.5 32.1 - - + -
139A ASN* 1.3 74.6 + - - +
141A GLU* 1.3 62.9 - - - +
142A VAL* 4.1 16.6 - - + -
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Residues in contact with GLU 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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55A SER 4.5 0.2 - - - -
56A VAL* 3.4 3.5 - - - -
57A TYR* 3.0 69.2 + - + +
98A THR* 4.0 20.2 - - + +
99A LEU 3.7 4.9 - - - +
100A LEU* 4.5 11.1 - - + +
140A MET* 1.3 78.1 - - - +
142A VAL* 1.3 62.9 + - - +
143A ARG 3.9 1.4 + - - -
160A ASP* 4.6 12.5 - - - +
161A ARG* 3.6 24.3 + - - +
164A ALA* 5.2 0.2 - - - +
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Residues in contact with VAL 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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53A VAL* 3.3 28.9 - - + -
55A SER 3.2 15.7 - - - +
56A VAL* 3.4 18.6 - - + -
82A LEU* 3.4 21.3 - - + -
85A LEU* 5.8 0.9 - - + -
98A THR* 4.4 1.6 - - - -
99A LEU* 3.0 35.3 + - + +
114A PHE* 3.6 32.8 - - + -
140A MET* 4.1 13.5 - - + -
141A GLU* 1.3 75.5 - - - +
143A ARG* 1.3 62.5 + - - +
144A VAL* 3.9 3.0 + - + +
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Residues in contact with ARG 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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53A VAL* 3.4 7.8 - - - +
54A THR* 3.2 45.6 + - - +
55A SER* 2.9 24.2 + - - +
96A THR* 3.0 32.1 + - - +
97A VAL 3.9 4.5 - - - -
98A THR* 4.0 15.1 + - - +
141A GLU 3.9 2.6 + - - -
142A VAL* 1.3 73.9 - - - +
144A VAL* 1.3 72.1 + - - +
145A ASP* 3.2 20.2 + - - -
158A ILE* 3.4 38.2 - - - +
160A ASP* 3.7 19.3 + - - +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 4.5 1.8 - - - -
52A ALA 3.7 15.5 - - - +
53A VAL* 4.6 12.3 - - + -
54A THR* 4.1 0.4 - - - -
85A LEU* 5.1 2.2 - - + -
87A VAL* 3.3 36.1 - - + -
89A PHE* 4.5 9.2 - - + -
95A GLN 3.9 0.3 - - - +
96A THR* 3.4 6.1 + - - -
97A VAL* 2.9 45.3 + - + +
99A LEU* 4.8 17.3 - - + -
142A VAL* 3.9 7.9 - - + +
143A ARG* 1.3 83.8 - - - +
145A ASP* 1.3 69.8 + - - +
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Residues in contact with ASP 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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51A THR* 3.2 28.2 - - - +
52A ALA 3.2 6.6 + - - -
54A THR* 3.2 21.5 + - + +
89A PHE* 4.0 5.6 - - - -
95A GLN* 2.8 21.0 - - - +
96A THR* 3.4 5.4 - - - -
143A ARG* 3.2 25.5 + - - +
144A VAL* 1.3 74.8 - - - +
146A ARG* 1.3 74.4 + - - +
171A PHE* 3.3 17.4 - - + -
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Residues in contact with ARG 146 (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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49A PRO* 5.5 13.6 - - + +
50A GLY 3.3 11.4 - - - +
89A PHE* 3.3 34.7 - - + -
91A ASN* 4.1 5.7 + - - +
92A PRO* 3.8 40.9 - - - +
94A LEU 4.7 5.1 + - - +
95A GLN* 3.5 11.6 + - - +
145A ASP* 1.3 84.5 - - - +
147A GLY* 1.3 60.8 + - - +
171A PHE* 3.9 2.2 - - - -
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Residues in contact with GLY 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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49A PRO* 3.2 9.7 - - - +
50A GLY 3.0 25.0 + - - -
145A ASP* 5.3 0.2 - - - -
146A ARG* 1.3 75.5 - - - +
148A VAL* 1.3 66.5 + - - -
171A PHE* 3.1 29.2 - - - -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 4.2 4.0 - - - +
47A SER* 2.9 32.5 - - - +
48A ILE 3.7 9.9 - - - +
49A PRO* 3.7 12.8 - - + -
147A GLY* 1.3 78.0 - - - +
149A GLY* 1.3 69.5 + - - +
150A TYR 3.9 0.5 + - - +
151A VAL* 4.3 8.7 - - - +
171A PHE* 3.1 13.0 - - - -
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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