Contacts of the strand formed by residues 60 - 74 (chain A) in PDB entry 2W2R
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER* 4.1 9.9 - - - +
59A LEU* 1.3 78.0 - - - +
61A TYR* 1.3 70.0 + - - +
62A GLU* 3.2 32.7 + - - +
141A LEU 3.6 0.9 - - - +
142A PRO* 3.3 3.1 - - - +
143A HIS* 2.8 47.0 + - + +
146A GLY* 3.6 30.3 + - - -
147A LEU* 3.6 29.7 - - - +
148A ILE 5.3 1.0 - - - +
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Residues in contact with TYR 61 (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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59A LEU* 4.2 20.4 - - + +
60A ARG* 1.3 88.9 + - - +
62A GLU* 1.3 67.5 + - - +
63A LYS 4.0 1.0 + - - -
140A PHE* 3.9 40.9 - + + -
141A LEU 3.5 3.8 - - - +
142A PRO* 3.7 21.3 - - + -
188A HIS* 3.7 33.8 - + - -
217A THR* 4.7 5.9 + - - -
219A THR* 3.9 10.3 - - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.2 34.5 + - - -
61A TYR* 1.3 74.0 - - - +
63A LYS* 1.3 64.3 + - - +
64A PHE* 3.6 3.9 - - - -
104A PHE* 3.9 29.8 - - + -
139A CYS 3.5 1.0 - - - +
140A PHE* 3.2 4.0 - - - -
141A LEU 2.8 38.3 + - - +
143A HIS* 2.9 33.8 + - + +
148A ILE* 3.8 24.9 - - + +
151A MSE 5.0 5.6 - - + -
179A ASP* 5.9 1.6 - - - +
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Residues in contact with LYS 63 (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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61A TYR 4.0 2.4 + - - +
62A GLU* 1.3 73.8 + - - +
64A PHE* 1.3 64.1 + - - +
138A ARG* 4.5 0.2 - - - +
139A CYS 3.3 8.7 - - - +
140A PHE* 4.0 18.6 - - + -
151A MSE 5.6 0.2 - - - +
179A ASP* 4.0 7.4 - - - +
180A ASP* 3.3 53.4 + - - +
182A SER 2.8 26.2 + - - -
183A ASN* 4.2 3.6 + - - +
184A GLU 3.1 24.8 + - - -
185A LYS* 5.3 0.2 - - - +
186A VAL* 3.7 18.6 - - + -
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Residues in contact with PHE 64 (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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62A GLU 3.6 11.2 - - - -
63A LYS* 1.3 75.8 - - - +
65A ARG* 1.3 73.6 + - - +
66A PHE* 4.0 24.0 - + + -
104A PHE* 3.9 23.3 - + - -
107A ILE* 5.0 4.5 - - + -
108A ILE* 4.1 12.3 - - + -
138A ARG* 3.3 2.8 - - - +
139A CYS* 2.9 57.1 + - - +
140A PHE 4.4 0.4 - - - -
141A LEU* 3.8 26.7 - - + -
151A MSE 4.2 16.4 - - + -
177A VAL* 3.8 13.2 - - + -
178A SER 3.4 13.2 - - - +
180A ASP* 3.7 7.4 - - - +
189A VAL* 4.0 14.8 - - + -
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Residues in contact with ARG 65 (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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64A PHE* 1.3 80.1 - - - +
66A PHE* 1.3 63.5 + - - +
137A GLY 3.3 12.1 - - - +
138A ARG* 3.9 15.7 - - + +
153A ASN* 3.6 32.2 + - - +
176A THR 3.9 0.2 - - - +
177A VAL* 3.3 4.0 - - - -
178A SER* 2.6 73.7 + - - +
179A ASP 2.9 20.5 + - - +
180A ASP* 3.9 12.1 - - + +
181A GLU 5.6 0.2 - - - +
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Residues in contact with PHE 66 (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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64A PHE* 4.0 24.9 - + + -
65A ARG* 1.3 77.4 - - - +
67A MSE 1.3 68.2 + - - +
68A LEU* 4.0 18.8 - - + -
108A ILE* 4.0 24.9 - - + -
111A ILE* 5.3 2.9 - - + -
135A LEU* 3.9 30.3 - - + -
136A THR* 3.3 7.9 - - - -
137A GLY* 2.9 65.2 + - - +
139A CYS* 3.9 16.4 - - - -
176A THR* 3.0 11.2 - - - +
177A VAL* 4.2 3.4 - - + -
189A VAL* 5.1 2.7 - - + -
192A TYR* 4.1 18.4 - + + -
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Residues in contact with MSE 67 (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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66A PHE* 1.3 79.1 - - - +
68A LEU* 1.3 71.0 + - - +
69A LYS* 4.5 23.6 - - + -
108A ILE* 4.0 2.3 - - - +
134A THR* 5.3 1.3 - - - +
135A LEU 3.4 6.1 - - - +
136A THR* 3.6 24.7 - - + -
153A ASN* 6.2 0.2 - - - +
174A THR 3.9 0.8 - - - +
175A PHE* 3.5 3.5 - - - -
176A THR* 2.8 51.6 + - + +
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Residues in contact with LEU 68 (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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66A PHE* 4.0 22.4 - - + -
67A MSE 1.3 76.6 - - - +
69A LYS* 1.3 63.2 + - - +
70A MSE 3.7 23.6 - - + -
108A ILE* 3.4 32.5 - - + +
111A ILE* 5.2 0.7 - - + -
112A GLY* 3.9 15.9 - - - +
133A ALA* 3.9 13.5 - - + +
134A THR* 3.1 11.3 + - - -
135A LEU* 2.9 51.5 + - + +
174A THR 3.4 5.8 - - - -
175A PHE* 3.8 18.4 - - + -
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Residues in contact with LYS 69 (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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67A MSE 4.5 22.4 - - + -
68A LEU* 1.3 78.9 - - - +
70A MSE 1.3 62.7 + - - +
71A THR* 4.3 0.7 - - - -
132A TYR* 3.6 25.1 - - + +
133A ALA 3.5 4.9 - - - -
134A THR* 3.7 9.6 - - - +
172A ASP 3.8 2.1 - - - +
173A PHE* 3.3 2.6 - - - -
174A THR* 2.8 51.7 + - + +
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Residues in contact with MSE 70 (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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68A LEU* 3.7 23.1 - - + -
69A LYS* 1.3 79.4 - - - +
71A THR* 1.3 62.3 + - - +
88A VAL* 3.6 36.3 - - + -
108A ILE 4.2 0.2 - - - +
109A ALA* 3.6 15.0 - - - +
112A GLY* 3.8 17.5 - - - -
113A SER* 4.0 8.3 - - - +
116A LEU* 3.7 12.5 - - + +
132A TYR* 3.2 9.2 - - - -
133A ALA* 2.9 39.6 + - + +
172A ASP 3.7 2.9 - - - -
173A PHE* 3.6 28.0 - - + -
175A PHE* 3.9 21.1 - - + -
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Residues in contact with THR 71 (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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70A MSE 1.3 72.5 - - - +
72A VAL* 1.3 65.2 + - - +
73A ARG* 4.0 34.8 - - + +
130A GLU* 5.3 5.2 - - + +
131A TYR 3.3 10.8 - - - +
132A TYR* 3.4 22.3 - - + -
170A THR 4.0 0.3 - - - +
171A LEU* 3.5 3.5 - - - -
172A ASP* 2.9 47.2 + - - -
173A PHE* 3.6 4.0 - - - -
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Residues in contact with VAL 72 (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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71A THR* 1.3 79.0 - - - +
73A ARG* 1.3 67.1 + - - +
74A SER 4.2 0.2 - - - -
78A PHE* 3.9 25.4 - - + -
84A VAL* 5.9 0.2 - - + -
87A ALA* 4.9 2.2 - - + -
88A VAL* 4.0 10.5 - - + -
116A LEU* 3.9 26.9 - - + -
130A GLU* 3.3 2.9 - - - +
131A TYR* 2.8 48.0 + - + +
162A PHE* 3.8 24.2 - - + -
170A THR 3.5 2.2 - - - -
171A LEU* 3.9 17.5 - - + -
173A PHE* 4.0 6.7 - - + -
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Residues in contact with ARG 73 (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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71A THR* 4.0 21.6 + - + +
72A VAL* 1.3 77.0 - - - +
74A SER* 1.3 62.1 + - - +
129A PRO 3.5 7.0 - - - +
130A GLU* 3.9 25.7 + - + +
162A PHE* 3.4 4.5 - - - -
169A GLY* 3.1 5.9 - - - -
170A THR* 2.9 69.2 + - - +
171A LEU 4.8 0.6 + - - -
172A ASP* 3.6 35.3 + - - +
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Residues in contact with SER 74 (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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72A VAL 4.2 0.4 - - - -
73A ARG* 1.3 75.8 - - - +
75A ASN* 1.3 62.2 + - - +
76A LYS 3.3 19.7 - - - -
78A PHE* 3.9 30.7 - - - -
127A ASN 3.9 2.8 - - - +
128A GLN* 4.2 1.7 - - - -
129A PRO* 3.0 34.3 + - - +
131A TYR* 4.6 1.3 - - - -
162A PHE* 4.1 5.2 - - - -
167A TYR* 5.1 0.2 - - - -
168A LYS 3.5 6.3 - - - -
169A GLY* 5.1 0.7 - - - -
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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