Contacts of the strand formed by residues 54 - 66 (chain B) in PDB entry 2E7A
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 GLY 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B SER 3.8 0.2 + - - -
53B GLU* 1.3 78.6 - - - +
55B LEU* 1.3 61.0 + - - -
56B TYR* 3.3 11.6 - - - -
125B GLN* 3.3 16.5 - - - +
126B LEU 2.9 29.2 + - - -
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Residues in contact with LEU 55 (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 SER* 5.1 18.8 - - - -
11A MET* 5.1 4.5 - - + +
13A VAL* 4.0 30.3 - - + -
36A LEU* 3.5 35.4 - - + -
155A ILE* 4.3 10.3 - - + -
54B GLY* 1.3 73.6 - - - -
56B TYR* 1.3 59.9 + - - +
123B VAL* 4.2 9.6 - - + -
124B PHE 3.4 2.2 - - - -
125B GLN* 3.4 25.6 - - + +
156B ALA* 3.5 5.9 - - - +
157B LEU* 3.0 38.8 + - + +
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Residues in contact with TYR 56 (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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12B PRO* 4.0 14.8 - - + +
50B VAL* 3.2 23.3 - - + +
51B PRO* 3.5 11.3 - - + +
52B SER* 2.8 34.7 + - - -
53B GLU 4.6 0.4 + - - -
54B GLY* 3.3 23.8 - - - -
55B LEU* 1.3 76.3 - - - +
57B LEU* 1.3 62.4 + - - +
58B ILE* 3.7 10.5 + - + +
122B GLY 3.7 0.7 - - - +
123B VAL* 3.2 5.6 - - - -
124B PHE 2.8 31.3 + - - -
126B LEU* 3.8 28.0 - - + -
154B ILE* 4.1 23.8 - - + -
155B ILE 3.2 7.9 - - - +
156B ALA* 3.6 31.3 - - + +
157B LEU* 4.5 1.1 - - - +
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Residues in contact with LEU 57 (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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57A LEU* 4.0 30.3 - - + -
59A TYR* 5.5 2.0 - - + -
119A TYR* 5.7 2.2 - - - +
56B TYR* 1.3 71.8 - - - +
58B ILE* 1.3 67.6 + - - +
59B TYR* 4.5 14.2 - - + -
121B GLY* 4.9 1.6 - - - -
122B GLY* 3.5 22.2 - - - +
123B VAL* 4.2 6.5 - - + +
154B ILE* 3.1 4.5 - - - -
155B ILE* 2.9 52.3 + - + +
157B LEU* 4.1 19.0 - - + +
57C LEU* 4.1 28.3 - - + -
123C VAL* 5.0 0.4 - - + -
157C LEU* 5.4 1.6 - - + -
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Residues in contact with ILE 58 (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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56B TYR* 4.0 19.1 - - + +
57B LEU* 1.3 82.0 - - - +
59B TYR* 1.3 64.1 + - - +
80B ILE* 3.8 21.5 - - + -
93B LEU* 3.7 21.5 - - + -
94B LEU* 3.7 11.7 - - + -
121B GLY* 3.1 2.1 - - - -
122B GLY 2.9 32.9 + - - +
124B PHE* 3.4 25.4 - - + -
126B LEU* 4.4 3.8 - - + -
132B LEU* 4.0 14.1 - - + -
152B PHE* 5.5 0.9 - - + -
153B GLY 3.4 4.5 - - - -
154B ILE* 3.9 20.6 - - + -
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Residues in contact with TYR 59 (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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14B ALA 4.0 0.5 + - - -
15B HIS* 2.6 37.1 + - - +
57B LEU* 4.5 15.9 - - + -
58B ILE* 1.3 81.1 - - - +
60B SER* 1.3 67.4 + - - +
80B ILE* 3.8 5.8 - - - +
119B TYR* 3.4 15.5 - - - +
120B LEU 3.1 15.3 - - - +
121B GLY* 4.0 3.4 - - - -
151B TYR* 3.8 12.6 - + - -
152B PHE* 3.4 3.6 - - - -
153B GLY* 2.9 61.5 + - - +
154B ILE* 4.0 3.8 - - - -
57C LEU* 5.3 2.0 - - + -
121C GLY 3.6 13.9 - - - -
122C GLY* 3.7 16.8 - - - -
123C VAL* 3.0 33.7 + - + +
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Residues in contact with SER 60 (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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28B TRP* 4.1 2.4 - - - -
59B TYR* 1.3 81.0 - - - +
61B GLN* 1.3 62.4 + - - +
78B HIS* 3.0 30.4 + - - -
80B ILE* 3.7 17.0 - - - +
119B TYR* 3.5 3.2 - - - -
120B LEU* 2.8 33.7 + - - +
134B ALA* 3.9 6.3 - - - +
151B TYR* 2.7 25.0 + - - -
152B PHE* 4.0 8.1 - - - -
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Residues in contact with GLN 61 (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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60B SER* 1.3 75.3 + - - +
62B VAL* 1.3 76.7 + - - +
63B LEU* 4.9 2.4 - - - +
117B PRO* 5.2 3.3 - - + +
118B ILE 3.2 15.0 - - - +
119B TYR* 3.9 5.7 - - + -
148B GLY 3.7 2.0 + - - -
149B GLN* 2.9 22.6 + - - +
150B VAL* 3.3 2.9 - - - +
151B TYR* 2.7 73.7 + - + +
95C SER 2.9 25.9 + - - -
96C ALA* 3.9 10.8 - - - +
119C TYR 3.7 16.7 - - - +
120C LEU* 4.1 7.3 - - - +
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Residues in contact with VAL 62 (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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26B LEU* 4.6 7.0 - - + -
28B TRP* 4.8 0.7 - - + -
60B SER* 4.6 0.9 - - - +
61B GLN* 1.3 80.9 - - - +
63B LEU* 1.3 61.1 + - - +
64B PHE* 3.6 29.8 - - + -
78B HIS* 3.4 46.2 + - + +
116B GLU 4.1 0.4 - - - +
117B PRO* 3.4 2.9 - - - +
118B ILE* 2.9 32.4 + - + +
136B ILE* 3.7 15.3 - - + -
142B LEU* 4.2 8.3 - - + -
149B GLN 3.8 5.6 - - - -
150B VAL* 4.1 16.2 - - + -
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Residues in contact with LEU 63 (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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61B GLN* 4.9 0.7 - - - +
62B VAL* 1.3 75.3 - - - +
64B PHE* 1.3 65.7 + - - +
115B TYR* 4.0 20.2 - - + -
116B GLU 3.6 9.9 - - - +
117B PRO* 3.6 24.0 - - + -
142B LEU* 3.3 7.4 - - - +
143B ASP* 2.8 36.0 + - + +
149B GLN* 3.6 50.2 + - + +
150B VAL* 4.1 2.8 - - - +
96C ALA* 4.5 4.3 - - + -
97C ILE* 3.6 37.9 - - + +
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Residues in contact with PHE 64 (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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62B VAL* 3.6 18.6 - - + -
63B LEU* 1.3 78.3 - - - +
65B SER* 1.3 60.5 + - - +
76B LEU* 3.6 54.1 - - + -
77B THR 3.7 11.9 - - - -
114B TRP* 3.9 4.9 - - + -
115B TYR* 3.3 3.5 - - - -
116B GLU 2.8 42.7 + - - +
118B ILE* 3.9 16.8 - - + -
136B ILE* 3.7 35.9 - - + -
137B ASN* 4.5 0.4 - - - -
138B ARG* 3.7 18.4 - - + -
141B TYR* 3.1 24.0 - - + +
142B LEU* 4.1 3.4 - - + -
143B ASP* 4.5 1.1 - - - -
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Residues in contact with SER 65 (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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64B PHE* 1.3 75.8 - - - +
66B GLY* 1.3 59.2 + - - +
114B TRP* 3.1 22.6 - - - -
115B TYR* 3.7 17.0 - - - -
140B ASP 5.1 0.3 - - - +
141B TYR* 2.7 32.4 + - - +
142B LEU 5.1 0.5 + - - -
143B ASP* 2.7 32.5 + - - +
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Residues in contact with GLY 66 (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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65B SER* 1.3 76.0 - - - +
67B GLN* 1.3 59.3 + - - -
68B GLY 3.0 9.8 + - - -
113B PRO* 3.1 2.5 - - - +
114B TRP* 2.8 54.0 + - - -
141B TYR* 4.9 5.8 - - - -
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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