Contacts of the strand formed by residues 124 - 131 (chain B) in PDB entry 5MR4
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 THR 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 5.1 4.1 - - + +
110B VAL 3.1 16.2 - - - +
111B ARG* 4.7 15.5 - - - +
122B ASP 4.4 6.5 - - - +
123B GLU* 1.3 78.7 + - - +
125B VAL* 1.3 63.7 + - - +
166D LYS* 3.5 51.6 - - + +
169D ASN* 3.2 28.4 + - - +
170D LEU* 4.2 12.1 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 3.6 2.9 - - - -
110B VAL* 2.8 53.2 + - + +
112B VAL* 3.7 23.3 - - + -
115B LEU* 4.5 1.8 - - + -
124B THR* 1.3 79.9 + - - +
126B LEU* 1.3 61.8 + - - +
127B PHE* 3.4 7.2 + - + +
174B VAL* 3.8 35.0 - - + -
176B PHE* 4.6 5.4 - - + -
189B LEU* 4.4 19.1 - - + -
169D ASN* 3.9 11.0 - - - +
170D LEU* 4.3 5.6 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 4.0 34.1 - - + +
108B LEU 3.7 10.5 - - - +
109B GLU* 4.2 13.0 - - + +
125B VAL* 1.3 74.5 - - - +
127B PHE* 1.3 61.0 + - - +
128B ARG* 3.3 39.0 + - + +
171B GLU* 4.8 6.6 - - - +
190B SER* 3.3 11.1 + - - -
169D ASN 4.4 10.5 + - - +
170D LEU* 3.9 37.7 - - + +
172D ASP* 4.9 2.7 - - - +
175D LYS* 6.1 2.8 - - + +
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Residues in contact with PHE 127 (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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141A TYR* 4.1 27.6 - + - -
144A GLY 5.0 0.7 - - - -
145A LEU* 3.8 31.2 - - + -
148A LEU* 3.5 28.3 - - + -
106B ARG 3.9 0.2 - - - +
107B GLU* 3.5 1.6 - - - -
108B LEU* 2.8 43.6 + - + +
110B VAL* 4.0 17.9 - - + -
115B LEU* 4.8 7.9 - - + -
125B VAL* 3.4 4.6 + - + -
126B LEU* 1.3 72.0 - - - +
128B ARG* 1.3 60.8 + - - +
129B TYR* 3.9 18.6 - + + -
189B LEU* 3.3 42.0 - - + -
190B SER* 3.3 11.0 - - - -
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Residues in contact with ARG 128 (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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141A TYR* 3.7 3.6 - - - -
105B LEU* 4.2 23.3 - - + -
106B ARG 3.1 7.0 - - - +
107B GLU* 3.4 34.5 + - + +
126B LEU* 3.3 28.9 - - + +
127B PHE* 1.3 77.1 - - - +
129B TYR* 1.3 63.3 + - - +
171B GLU* 5.6 1.4 + - - -
190B SER* 2.8 17.6 + - - +
191B ALA* 2.9 43.2 + - - +
192B ARG* 5.6 7.6 - - - +
172D ASP* 3.0 38.7 + - - -
175D LYS* 5.1 6.7 - - - +
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Residues in contact with TYR 129 (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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141A TYR* 3.4 18.2 - - + +
145A LEU* 3.7 22.7 - - + -
153A ARG 5.4 0.2 + - - -
154A LEU* 3.9 34.5 - - + +
155A ARG* 4.0 21.8 + - - +
157A GLU* 5.3 0.6 + - - -
159A VAL* 4.4 5.2 - - + -
104B GLY 3.6 0.2 - - - +
105B LEU* 3.4 6.5 - - - -
106B ARG* 2.8 66.4 + - + +
107B GLU 4.3 3.0 + - - -
108B LEU* 4.4 17.9 - - + +
127B PHE* 3.9 18.2 - + + -
128B ARG* 1.3 77.6 - - - +
130B CYS* 1.3 73.2 + - - +
131B ALA* 3.8 15.5 - - + -
191B ALA* 4.0 2.2 - - - -
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Residues in contact with CYS 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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141A TYR* 3.1 13.3 + - - +
145A LEU* 5.1 1.7 - - - +
159A VAL* 4.6 9.5 - - - +
160A ARG 4.7 3.8 + - - +
104B GLY 3.4 3.8 - - - -
129B TYR* 1.3 77.7 - - - +
131B ALA* 1.3 64.5 + - - +
165B CYS* 4.0 18.0 - - - +
166B ARG* 4.1 10.8 - - - -
167B PRO* 3.6 26.9 - - + -
191B ALA* 3.9 6.1 - - - -
193B GLU 3.8 1.8 - - - -
194B CYS* 2.1 52.7 - - + -
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Residues in contact with ALA 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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157A GLU* 3.7 16.2 - - - +
158A ARG 3.5 14.4 - - - +
159A VAL* 3.7 15.9 - - + +
103B CYS* 3.3 0.3 - - - -
104B GLY 2.8 32.5 + - - +
106B ARG* 3.3 12.0 + - + -
129B TYR* 3.8 15.0 + - + -
130B CYS* 1.3 76.0 - - - +
132B GLY* 1.3 61.7 + - - +
165B CYS* 3.8 7.3 - - - -
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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