Contacts of the strand formed by residues 111 - 126 (chain R) in PDB entry 4M8B
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 TYR 111 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R TYR* 4.2 21.5 - + + -
85R ASN 3.1 20.6 - - - +
86R ARG* 3.5 36.7 + - + -
87R LEU* 3.9 3.8 - - - -
103R ILE* 3.3 8.7 - - - +
104R PHE* 2.7 73.1 + + + +
106R ARG* 4.2 18.4 - - + -
109R ARG* 4.1 29.5 - - + +
110R LYS* 1.3 74.3 - - - +
112R PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R TYR* 3.0 6.3 - - - -
85R ASN* 2.8 85.4 + - + -
86R ARG 3.5 15.9 - - - -
87R LEU* 4.0 18.8 - - + -
96R HIS* 4.4 14.1 - + - -
98R VAL* 3.8 42.8 - - + -
102R ASN 3.3 11.7 - - - +
103R ILE* 4.2 7.0 - - + -
104R PHE* 4.4 1.8 - - - -
111R TYR* 1.3 76.7 - - - +
113R TYR* 1.3 73.0 + - - +
114R THR* 4.2 15.3 - - + -
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Residues in contact with TYR 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R SER* 4.2 17.7 - - - -
71R PRO* 5.5 1.9 - - - +
82R ARG* 3.0 64.6 - - + +
83R GLU 3.4 13.5 - - - +
84R TYR* 3.9 10.3 - + + -
98R VAL* 5.4 2.4 - - - +
99R PRO* 6.2 0.2 - - - +
101R TYR 5.2 1.8 - - - -
102R ASN* 2.8 52.4 + - + +
104R PHE* 3.6 38.2 - + + -
106R ARG* 5.6 1.9 + - - -
112R PHE* 1.3 80.5 - - - +
114R THR* 1.3 63.5 + - - +
115R GLY 3.7 2.6 + - - +
146R GLU* 5.2 0.2 - - - +
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Residues in contact with THR 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R GLU* 2.5 46.8 + - - +
85R ASN* 3.6 35.0 - - - +
102R ASN* 5.5 0.4 - - - -
112R PHE* 4.2 15.9 - - + -
113R TYR* 1.3 74.8 - - - +
115R GLY* 1.3 59.4 + - - +
116R LEU* 3.3 9.3 + - - +
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Residues in contact with GLY 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R GLU 4.5 0.6 + - - -
102R ASN* 5.4 1.1 - - - -
113R TYR* 3.4 4.4 - - - +
114R THR* 1.3 78.9 + - - +
116R LEU* 1.3 65.2 + - - +
117R LEU* 3.6 2.2 + - - +
145R THR* 3.0 22.8 + - - -
146R GLU* 3.1 45.3 + - - +
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Residues in contact with LEU 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 3.7 43.7 - - + +
47R PRO* 4.2 17.9 - - + -
67R PHE* 5.1 0.9 - - + -
69R TRP* 3.9 22.7 - - + -
82R ARG* 4.0 1.0 - - - +
83R GLU* 3.3 53.0 + - + +
114R THR* 3.3 3.2 + - - +
115R GLY* 1.3 81.0 + - - +
117R LEU* 1.3 66.6 - - - +
143R TYR* 4.7 2.0 - - + -
144R TYR 3.4 20.0 - - - +
145R THR* 4.1 3.8 + - - -
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Residues in contact with LEU 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R TRP* 4.2 4.5 - - - -
80R VAL* 4.4 9.2 - - + -
81R TYR 3.5 6.5 - - - +
82R ARG* 3.4 41.3 - - + -
115R GLY 3.7 4.3 - - - +
116R LEU* 1.3 79.7 - - - +
118R LYS* 1.3 61.1 + - - +
143R TYR* 3.4 8.1 - - - +
144R TYR* 2.7 71.5 + - + +
146R GLU* 3.7 33.4 - - + +
149R ILE* 5.5 1.3 - - + -
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Residues in contact with LYS 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A G 4.9 5.1 + - - +
10A T 4.7 8.9 + - - +
63R TRP* 4.6 12.6 + - + -
65R ASP* 3.0 21.2 + - - -
69R TRP* 3.1 45.5 - - + +
80R VAL* 3.3 4.6 - - - +
81R TYR* 2.9 50.5 + - + +
117R LEU* 1.3 75.4 - - - +
119R LYS* 1.3 62.4 + - - +
120R THR* 4.0 14.1 - - + -
141R ILE* 3.6 31.2 - - + -
142R ALA 3.3 5.8 - - - +
143R TYR* 3.9 11.4 + - + +
144R TYR* 4.3 2.2 - - - -
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Residues in contact with LYS 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R TYR* 3.6 17.0 + - + -
11R ILE* 3.0 31.9 + - + +
12R ASP* 4.6 5.5 + - - +
75R SER* 5.6 4.0 + - - -
78R PHE* 3.9 37.0 - - + -
79R LEU 3.0 10.3 - - - +
80R VAL* 4.2 8.7 - - + +
118R LYS* 1.3 75.1 - - - +
120R THR* 1.3 65.9 + - - +
140R LEU* 3.8 2.2 - - + +
141R ILE* 3.7 0.5 - - - -
142R ALA* 3.0 48.5 + - + +
144R TYR* 3.5 32.6 + - + +
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Residues in contact with THR 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A T 4.0 15.7 + - - +
11A G 4.9 1.4 + - - -
77R LYS 4.4 0.5 - - - +
78R PHE* 3.4 9.9 - - - -
79R LEU* 2.9 53.0 + - - +
81R TYR* 3.9 9.2 + - + -
118R LYS* 4.0 15.3 - - + -
119R LYS* 1.3 77.9 - - - +
121R PHE* 1.3 63.5 + - - +
140R LEU* 3.1 7.2 - - - -
141R ILE* 3.4 24.5 - - + -
301R EDO 3.7 14.7 - - - -
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Residues in contact with PHE 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A G 5.5 0.2 - - - -
14R GLU* 5.8 1.8 - - + -
17R LEU* 3.4 27.4 - - + -
21R PHE* 3.8 17.3 - + - -
77R LYS* 3.8 39.7 - - + -
78R PHE* 3.8 17.0 - + + -
120R THR* 1.3 75.7 - - - +
122R SER* 1.3 81.3 + - - +
123R LEU* 3.8 7.4 - - + -
138R PHE 3.8 0.5 - - - +
139R HIS 3.6 0.2 - - - -
140R LEU* 2.8 37.1 + - + +
176R LEU* 3.5 34.3 - - + -
179R VAL* 4.1 20.2 - - + -
301R EDO 2.9 7.8 + - - -
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Residues in contact with SER 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A G 3.5 27.4 + - - -
121R PHE* 1.3 88.1 - - - +
123R LEU* 1.3 61.2 + - - +
124R LYS* 4.3 5.6 + - - +
137R THR* 4.7 13.5 - - - -
138R PHE 3.4 6.1 - - - -
139R HIS* 5.1 2.2 - - - -
179R VAL* 4.3 13.0 - - - +
301R EDO 3.2 15.5 - - - -
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Residues in contact with LEU 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R PHE* 3.7 28.9 - - + -
25R PHE* 4.4 5.8 - - + -
121R PHE* 3.8 9.6 - - + -
122R SER* 1.3 75.3 - - - +
124R LYS* 1.3 67.4 + - - +
125R PHE* 4.1 15.5 - - + -
136R GLU 3.7 1.2 - - - +
137R THR* 3.5 1.6 - - - +
138R PHE* 2.8 44.1 + - + +
172R LEU* 3.5 29.4 - - + -
175R ALA* 4.0 30.5 - - + +
176R LEU* 3.7 19.7 - - + -
179R VAL* 4.4 7.0 - - + -
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Residues in contact with LYS 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R GLU* 5.6 0.8 + - - -
122R SER* 5.7 5.4 - - - +
123R LEU* 1.3 80.0 - - - +
125R PHE* 1.3 62.4 + - - +
135R LEU* 4.3 26.1 - - + +
136R GLU 3.3 7.4 - - - +
137R THR* 3.4 32.2 + - + +
175R ALA* 4.5 6.9 - - - +
179R VAL* 5.6 2.6 - - - +
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Residues in contact with PHE 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R PHE* 3.7 19.5 - + - -
123R LEU* 3.8 14.1 + - + -
124R LYS* 1.3 73.7 - - - +
126R ASN* 1.3 84.4 + - - +
127R MET* 3.2 34.3 + - + +
135R LEU* 4.1 6.7 - - - +
136R GLU* 3.0 29.0 + - - +
138R PHE* 4.3 9.1 - - + -
169R SER* 4.6 3.8 - - - -
171R LYS* 3.2 55.0 - - + -
172R LEU* 3.5 23.1 - - + -
175R ALA* 3.7 19.3 - - + -
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Residues in contact with ASN 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125R PHE* 1.3 92.5 - - - +
127R MET* 1.3 62.7 + - - +
130R THR* 2.7 34.1 + - - +
131R ASP 4.5 1.0 + - - -
132R SER 3.5 16.4 + - - -
133R THR* 4.2 3.5 - - - +
134R LYS 3.7 13.3 + - - -
135R LEU* 3.7 19.4 - - + +
171R LYS* 3.1 31.9 + - + +
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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
------------------------------------------------------------
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