Contacts of the strand formed by residues 54 - 67 (chain A) in PDB entry 3WD5
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER 3.4 1.4 + - - -
53A GLU* 1.3 79.9 - - - +
55A LEU* 1.3 67.1 + - - -
56A TYR* 3.5 9.8 - - - -
125A GLN* 3.5 6.9 - - - +
126A LEU 3.0 32.0 + - - +
156A ALA* 6.4 0.2 - - - -
157A LEU 5.6 1.1 - - - -
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Residues in contact with LEU 55 (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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54A GLY* 1.3 72.8 - - - -
56A TYR* 1.3 61.2 - - - +
123A VAL* 4.4 16.2 - - + -
124A PHE 3.5 4.3 - - - +
125A GLN* 4.0 29.2 - - + +
156A ALA* 3.6 5.5 - - - +
157A LEU* 3.0 48.7 + - + +
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Residues in contact with TYR 56 (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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12A PRO* 4.2 11.3 - - + +
50A VAL* 3.5 20.0 - - + +
51A PRO* 3.9 7.8 - - + +
52A SER* 2.8 43.5 + - - -
53A GLU 4.7 0.2 + - - -
54A GLY* 3.5 23.3 - - - -
55A LEU* 1.3 73.1 - - - +
57A LEU* 1.3 62.6 + - - +
58A ILE* 3.7 15.7 + - + +
123A VAL* 3.4 5.5 - - - +
124A PHE 2.9 33.0 + - - +
126A LEU* 3.9 23.1 - - + -
154A ILE* 4.1 23.3 - - + -
155A ILE 3.3 6.3 - - - -
156A ALA* 3.5 36.5 - - + +
157A LEU 4.7 0.2 - - - +
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Residues in contact with LEU 57 (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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56A TYR* 1.3 72.5 - - - +
58A ILE* 1.3 76.0 + - - +
59A TYR* 4.6 13.4 - - + +
121A GLY* 4.8 2.9 - - - -
122A GLY* 3.5 23.6 - - - +
123A VAL* 4.4 9.0 - - + +
153A GLY 4.5 0.2 - - - -
154A ILE* 3.0 6.9 - - - +
155A ILE* 2.9 51.8 + - + +
157A LEU* 4.2 18.9 - - + +
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Residues in contact with ILE 58 (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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56A TYR* 3.8 12.3 - - + +
57A LEU* 1.3 80.1 - - - +
59A TYR* 1.3 64.5 + - - +
80A ILE* 3.6 27.1 - - + -
93A LEU* 3.9 16.8 - - + -
94A LEU* 3.9 3.6 - - + +
121A GLY* 3.3 3.3 - - - -
122A GLY 3.0 29.6 + - - +
124A PHE* 3.5 33.0 - - + -
126A LEU* 4.2 7.4 - - + -
132A LEU* 3.8 24.2 - - + -
152A PHE* 3.8 7.2 - - + -
153A GLY 3.5 10.1 - - - +
154A ILE* 3.8 11.2 - - + -
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Residues in contact with TYR 59 (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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14A ALA 4.1 0.7 + - - -
15A HIS* 2.4 52.1 + + - +
57A LEU* 4.6 18.4 - - + -
58A ILE* 1.3 77.8 - - - +
60A SER* 1.3 60.7 - - - +
80A ILE* 3.9 3.8 - - - -
119A TYR* 3.4 20.6 - - + +
120A LEU 3.0 13.2 - - - +
121A GLY* 4.2 2.5 - - - -
151A TYR* 3.6 20.0 - + - -
152A PHE* 3.2 6.6 - - - -
153A GLY* 2.7 62.7 + - - +
154A ILE* 3.9 6.1 - - - -
155A ILE* 5.2 6.3 - - + -
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Residues in contact with SER 60 (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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28A TRP* 4.3 2.1 - - - -
59A TYR* 1.3 78.6 - - - +
61A GLN* 1.3 59.8 + - - +
78A HIS* 2.9 32.5 + - - -
80A ILE* 3.8 17.7 - - - -
118A ILE 3.9 0.5 - - - +
119A TYR* 3.8 3.1 - - - -
120A LEU* 2.8 32.7 + - - +
134A ALA* 4.0 3.1 - - - +
151A TYR* 2.9 23.6 + - - -
152A PHE* 3.9 11.8 - - - +
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Residues in contact with GLN 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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28A TRP* 4.8 0.5 - - - -
60A SER* 1.3 76.3 + - - +
62A VAL* 1.3 71.0 + - - +
63A LEU* 4.6 7.3 - - - +
78A HIS* 4.1 1.6 - - - -
117A PRO* 4.7 11.6 - - - +
118A ILE 3.4 8.3 - - - +
119A TYR* 3.8 16.3 - - + +
148A GLY 4.2 2.4 + - - -
149A GLN* 2.7 32.1 + - - +
150A VAL* 3.2 3.6 - - - +
151A TYR* 2.8 69.5 + - + +
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Residues in contact with VAL 62 (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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26A LEU* 4.2 12.1 - - + -
28A TRP* 5.7 0.2 - - + -
61A GLN* 1.3 78.1 - - - +
63A LEU* 1.3 58.0 + - - +
64A PHE* 3.4 29.2 - - + -
78A HIS* 3.7 27.8 - - + +
117A PRO* 3.3 3.8 - - - +
118A ILE* 2.9 38.1 + - + +
136A ILE* 3.7 19.1 - - + -
142A LEU* 3.4 27.4 - - + -
149A GLN 4.2 2.2 - - - -
150A VAL* 4.0 7.2 - - + -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLN* 4.6 4.0 - - - +
62A VAL* 1.3 77.0 - - - +
64A PHE* 1.3 76.5 + - - +
115A TYR* 4.1 17.3 - - + -
116A GLU 3.8 4.5 - - - +
117A PRO* 3.7 27.8 - - + -
142A LEU* 3.6 7.8 - - - +
143A ASP* 2.9 56.7 + - + +
149A GLN* 3.5 48.5 + - + +
150A VAL* 4.3 3.9 - - + +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.4 27.4 - - + -
63A LEU* 1.3 76.5 - - - +
65A LYS* 1.3 61.9 - - - +
76A LEU* 3.5 43.5 - - + -
77A THR 3.9 16.8 - - - -
114A TRP* 3.9 15.0 - - + -
115A TYR* 3.3 3.5 - - - -
116A GLU* 2.7 48.3 + - + +
118A ILE* 3.8 15.7 - - + -
136A ILE* 3.9 16.4 - - + -
137A ASN* 4.4 1.6 - - - -
138A ARG 3.7 17.7 - - - -
141A TYR* 3.2 23.6 - - + +
142A LEU* 4.2 8.3 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 1.3 76.0 - - - +
66A GLY* 1.3 54.1 + - - +
114A TRP* 3.2 24.4 - - - +
115A TYR* 3.7 24.4 + - + -
141A TYR* 2.6 15.8 + - - +
142A LEU 4.3 4.3 - - - +
143A ASP* 3.3 40.0 + - + +
144A PHE 5.3 0.2 - - - +
103H SER* 5.5 0.2 + - - -
105H ALA* 3.8 11.5 + - - +
30L ARG* 2.3 33.9 + - - +
32L TYR* 3.3 35.8 - - + +
92L ASN* 2.5 34.6 + - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LYS* 1.3 77.3 - - - +
67A GLN* 1.3 54.9 + - - -
113A PRO* 3.5 4.0 - - - +
114A TRP* 2.7 52.0 + - - +
30L ARG* 3.6 12.3 - - - -
32L TYR* 3.2 15.5 + - - -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLY* 1.3 76.3 - - - +
68A GLY* 1.3 65.8 + - - +
111A ALA* 4.1 7.6 - - - +
112A LYS 3.1 8.3 - - - +
113A PRO* 4.3 18.2 - - + +
114A TRP* 3.9 0.6 - - - +
30L ARG* 5.3 0.8 - - - +
31L ASN* 3.0 68.9 + - - +
32L TYR* 3.7 23.5 + - + +
49L TYR* 5.0 2.9 - - - -
50L ALA* 3.8 14.9 - - + +
91L TYR* 2.6 30.5 + - - -
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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