Contacts of the strand formed by residues 78 - 90 (chain A) in PDB entry 5FJV
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 MET 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ASP 4.5 0.2 - - - +
72A VAL* 3.1 18.6 - - - +
73A ASP 3.2 11.5 + - - +
76A ASN* 3.4 35.4 - - + +
77A GLN* 1.3 79.7 - - - +
79A MET* 1.3 66.1 + - - +
80A THR* 5.8 1.6 - - - +
126A ASP* 3.4 27.8 - - - +
154A LYS* 4.9 12.6 - - + -
155A SER 3.6 12.3 - - - +
156A SER* 4.1 7.0 - - - -
157A CYS* 4.1 2.7 - - - +
68B GLN* 5.9 0.2 - - - +
70B ILE* 4.5 14.8 - - + +
71B ASP* 6.2 0.9 - - + -
204B GLU* 4.3 7.9 - - - +
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.5 33.4 - - + -
71A ASP 3.6 2.9 - - - -
72A VAL* 3.9 11.2 - - + -
78A MET* 1.3 75.8 - - - +
80A THR* 1.3 63.9 + - - +
81A THR* 3.9 13.7 - - + -
153A TYR 3.7 0.9 - - - +
154A LYS* 3.4 4.3 - - - +
155A SER* 2.8 55.2 + - - +
156A SER 5.3 0.2 - - - +
157A CYS* 4.6 1.3 - - + +
171A CYS* 3.2 54.3 - - + +
172A LYS 4.7 0.9 - - - +
173A MET* 4.5 10.5 - - + -
207A ILE* 5.1 1.6 - - - -
233A PHE* 4.7 9.4 - - + -
235A ILE* 4.9 1.3 - - - -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.5 3.1 - - - +
70A ILE* 2.5 60.7 + - + -
71A ASP* 2.6 27.6 + - - +
78A MET* 5.8 1.4 - - - +
79A MET* 1.3 71.9 + - - +
81A THR* 1.3 63.1 + - - +
152A ILE* 4.4 11.9 - - + -
153A TYR 3.3 5.6 - - - +
154A LYS* 3.5 23.3 - - + +
126E ASP* 4.7 3.6 - - - +
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Residues in contact with THR 81 (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 ILE* 5.0 10.8 - - + -
68A GLN 3.6 4.9 - - - +
69A LEU* 3.9 27.1 - - + -
70A ILE* 3.8 3.6 - - - -
79A MET* 3.9 15.2 - - + +
80A THR* 1.3 78.5 - - - +
82A ASN* 1.3 60.3 + - - +
83A VAL* 3.9 16.0 - - + +
151A ALA 3.8 0.2 - - - +
152A ILE* 3.3 7.4 - - - +
153A TYR* 2.9 46.4 + - - +
155A SER* 4.7 3.8 + - - -
173A MET* 4.2 16.0 - - - +
233A PHE* 5.4 1.1 - - + -
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Residues in contact with ASN 82 (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 ALA* 2.9 36.5 + - - +
68A GLN* 2.7 18.5 + - + +
70A ILE* 3.4 21.2 - - + +
81A THR* 1.3 70.1 - - - +
83A VAL* 1.3 67.0 + - - +
84A TRP* 4.3 4.3 + - - -
151A ALA 3.4 7.2 - - - +
152A ILE* 3.4 12.5 - - + +
122E TYR 3.0 16.4 + - - +
123E ASN* 4.0 1.8 - - - +
124E ASN* 2.7 35.6 - - - +
129E PHE* 4.1 8.3 - - - -
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Residues in contact with VAL 83 (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 LEU* 3.7 23.6 - - + -
65A SER 3.2 13.9 - - - +
66A ILE* 4.1 17.0 - - + -
67A ALA 4.3 0.2 - - - +
81A THR* 3.9 24.2 - - - +
82A ASN* 1.3 79.6 - - - +
84A TRP* 1.3 74.7 + - - +
85A LEU* 4.7 2.7 - - + -
151A ALA* 2.8 49.5 + - + +
153A TYR* 4.1 22.4 - - + -
173A MET* 4.9 6.7 - - + -
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Residues in contact with TRP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 3.6 0.7 - - - +
64A LEU* 3.7 1.7 - - - -
65A SER* 2.8 50.6 + - - +
67A ALA* 3.8 26.2 - - + +
82A ASN* 4.3 5.7 + - - -
83A VAL* 1.3 84.7 - - - +
85A LEU* 1.3 62.0 + - - +
86A LYS* 3.3 5.0 + - - +
148A VAL* 3.9 16.4 - - + -
149A PRO 3.7 4.3 - - - +
150A PRO* 4.2 3.3 - - + +
199A TYR* 2.9 48.2 - + + -
122E TYR* 4.3 14.1 + + + -
174E LYS* 5.7 0.4 - - - -
178E TRP* 3.1 40.5 - + - -
219E TYR* 3.7 17.3 - + - -
221E CYS* 4.3 10.1 - - + -
300E EPJ 3.5 25.8 - - + -
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Residues in contact with LEU 85 (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 PHE* 3.3 31.4 - - + -
63A GLY 3.8 0.4 - - - +
64A LEU* 3.2 30.1 - - + -
83A VAL* 4.2 6.5 - - + -
84A TRP* 1.3 70.5 - - - +
86A LYS* 1.3 63.0 + - - +
87A GLN* 3.3 18.7 + - - +
119A ILE* 4.7 9.6 - - + +
131A VAL* 4.9 15.3 - - + +
147A TRP 3.3 13.0 - - - +
148A VAL* 3.7 3.1 - - - +
149A PRO* 3.2 28.7 + - + +
151A ALA* 5.5 2.2 - - + -
153A TYR* 4.1 14.6 - - + +
175A PHE* 3.8 24.7 - - + -
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Residues in contact with LYS 86 (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 ARG 4.0 0.4 - - - -
62A PHE* 3.3 10.6 - - - -
63A GLY* 2.7 64.7 + - - +
64A LEU 3.7 6.2 + - - +
65A SER* 3.4 23.0 + - - +
84A TRP 4.2 3.6 - - - +
85A LEU* 1.3 68.8 - - - +
87A GLN* 1.3 59.7 + - - +
147A TRP 3.9 3.6 - - - -
148A VAL* 4.3 19.7 - - + -
190A MET* 3.5 20.0 - - + +
194A VAL* 2.9 55.1 + - + +
221E CYS* 4.1 13.5 - - + +
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Residues in contact with GLN 87 (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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60A VAL* 4.3 9.0 - - + -
61A ARG 3.2 4.9 - - - +
62A PHE* 4.1 12.0 - - + -
85A LEU* 3.9 24.1 - - - +
86A LYS* 1.3 79.2 - - - +
88A GLU* 1.3 63.0 + - - +
89A TRP* 3.6 19.2 - - + -
117A PRO* 3.6 15.2 + - - +
119A ILE* 3.9 30.6 - - + +
131A VAL* 5.3 3.8 - - - +
145A VAL 3.8 0.2 - - - +
146A HIS* 3.7 1.2 - - - -
147A TRP* 2.9 68.8 + - - +
148A VAL* 4.9 0.9 - - - +
149A PRO* 5.5 0.6 - - - +
190A MET* 4.4 1.8 - - - -
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Residues in contact with GLU 88 (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 ILE 4.2 0.3 - - - +
60A VAL* 3.7 0.5 - - - +
61A ARG* 2.6 89.5 + - + +
87A GLN* 1.3 75.8 - - - +
89A TRP* 1.3 64.2 + - - +
144A THR* 5.2 5.6 - - + +
145A VAL 3.0 15.7 - - - +
146A HIS* 3.5 32.8 + - + +
190A MET* 3.5 7.8 - - + +
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Residues in contact with TRP 89 (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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52A PRO* 4.7 0.7 - - + -
58A VAL* 4.8 4.3 - - + -
59A ILE 3.8 17.3 - - - +
60A VAL* 4.3 11.4 - - + -
87A GLN* 3.6 36.8 - - + -
88A GLU* 1.3 83.0 - - - +
90A SER* 1.3 77.3 + - - +
91A ASP* 4.2 5.5 - - + +
114A ILE* 4.4 1.3 - - + -
115A TRP* 3.4 50.7 + + - -
116A ILE* 4.1 6.1 - - + -
117A PRO* 3.9 17.7 - - + -
144A THR* 3.5 8.8 - - - +
145A VAL* 2.8 62.1 + - + +
147A TRP* 3.7 27.4 - + + -
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Residues in contact with SER 90 (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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52A PRO* 3.6 16.5 - - - +
58A VAL* 5.1 5.1 - - - +
59A ILE 4.6 3.0 + - - -
89A TRP* 1.3 84.1 - - - +
91A ASP* 1.3 63.4 + - - +
92A TYR* 3.9 3.3 + - - +
95A ARG* 6.1 0.2 - - - -
142A THR 4.7 4.3 + - - -
143A GLY 3.5 11.3 + - - -
144A THR* 4.5 5.2 + - - +
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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