Contacts of the strand formed by residues 127 - 134 (chain B) in PDB entry 3OTC
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 PHE 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 3.4 12.0 - - - +
99A HIS* 3.6 12.9 + - - -
102A SER* 2.9 28.0 + - - +
28B LEU* 4.5 17.7 - - + -
29B ASP 3.6 5.6 - - - +
30B GLY* 3.6 20.4 - - - -
31B ARG* 4.1 0.4 - - - +
33B PHE* 3.9 29.2 - + - -
54B MET* 4.5 7.9 - - + -
101B ALA* 5.0 2.0 - - - +
104B PHE* 3.8 24.9 - + - -
105B ALA* 3.9 36.6 - - + -
108B TYR* 4.0 22.2 - + - -
125B PRO* 4.1 17.7 - - + -
126B GLY* 1.3 78.1 - - - -
128B ASP* 1.3 60.3 - - - +
129B GLY 4.0 0.2 + - - -
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 5.4 0.9 - - - -
95A LYS* 3.1 42.4 - - - +
98A THR* 3.9 3.3 + - - -
99A HIS* 3.6 20.6 + - + +
27B ARG 3.7 0.7 - - - +
28B LEU* 3.2 6.2 - - - -
29B ASP* 2.7 53.5 + - + +
31B ARG* 4.4 3.6 - - + +
127B PHE* 1.3 72.9 - - - +
129B GLY* 1.3 69.4 + - - +
130B ARG* 3.8 17.6 + - - -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.8 11.6 + - - +
95A LYS* 4.8 1.0 - - - +
98A THR* 3.1 40.5 + - - +
26B VAL* 5.4 2.0 - - - -
27B ARG 3.3 8.1 - - - -
28B LEU* 4.0 10.5 - - - -
97B MET* 4.9 0.2 - - - -
128B ASP* 1.3 82.6 + - - +
130B ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 4.0 25.4 + - - -
92A ARG* 5.5 10.3 - - - +
94A SER* 4.5 9.9 - - - +
95A LYS* 4.9 10.8 - - + +
26B VAL* 3.2 11.9 - - - +
27B ARG* 3.0 77.8 + - + +
29B ASP* 4.4 9.3 + - - -
97B MET* 4.1 8.8 - - - +
128B ASP* 3.8 21.2 + - - -
129B GLY* 1.3 77.0 - - - +
131B VAL* 1.3 65.6 + - - +
132B VAL* 4.5 9.9 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 5.1 1.6 - - - +
14A ALA* 5.0 8.8 + - - +
94A SER* 5.3 1.2 - - - -
18B CYS* 4.2 17.5 - - - -
24B VAL* 4.0 20.9 - - + -
25B VAL 3.4 2.7 - - - -
26B VAL* 3.9 16.8 - - + -
93B ALA* 4.0 18.6 - - + +
96B PHE* 4.3 3.8 - - + -
97B MET* 3.2 32.6 - - + +
130B ARG* 1.3 76.2 - - - +
132B VAL* 1.3 74.4 + - - +
133B VAL* 4.4 3.8 - - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.1 4.5 - - + -
13A GLU* 3.6 49.6 - - + +
14A ALA 5.8 0.2 - - - +
23B TRP 3.9 0.7 - - - +
24B VAL* 3.9 1.2 - - - -
25B VAL* 2.9 40.5 + - + +
27B ARG* 5.4 3.4 - - + +
130B ARG* 4.5 13.5 - - + -
131B VAL* 1.3 81.0 - - - +
133B VAL* 1.3 66.1 + - - +
134B TYR* 3.5 37.2 + - + +
143B TYR* 5.2 9.9 - - + +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.7 31.4 + - - +
14A ALA 6.0 0.2 - - - +
18B CYS* 4.1 32.5 - - + -
19B LEU* 4.6 13.7 - - + +
22B CYS* 3.4 31.9 - - + -
23B TRP 3.5 7.2 - - - +
24B VAL* 4.9 2.5 - - + -
131B VAL* 4.4 6.7 - - + -
132B VAL* 1.3 80.7 - - - +
134B TYR* 1.3 63.4 + - - +
135B PRO* 4.0 2.3 - - + +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 2.9 35.8 + - + +
12A PHE* 3.7 23.8 - + + -
13A GLU* 5.4 0.3 + - - +
22B CYS* 3.3 3.8 - - - +
23B TRP* 2.7 45.9 + - + +
25B VAL* 3.9 23.6 - - + -
132B VAL* 3.5 26.5 - - + +
133B VAL* 1.3 71.9 - - - +
135B PRO* 1.3 65.9 - - - +
136B SER 3.6 2.0 - - - +
139B THR* 3.6 30.7 - - - +
140B LEU* 4.3 14.6 - - + +
143B TYR* 2.8 45.5 - + + -
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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