Contacts of the strand formed by residues 75 - 89 (chain A) in PDB entry 3M4D
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 LYS 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 3.6 2.4 - - - +
71A GLU* 3.2 49.4 + - + +
72A GLY 2.9 16.8 + - - +
73A ALA 3.5 1.0 - - - -
74A ASN* 1.3 83.8 - - + +
76A SER* 1.3 68.0 + - - +
206A ALA* 3.5 3.1 - - - +
257A GLN* 3.6 32.7 + - - +
258A LEU 3.5 11.9 - - - +
259A HIS* 3.3 29.0 + - + +
268A THR* 5.3 4.0 - - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.3 9.7 - - - +
69A SER* 2.9 23.0 + - - -
70A GLU* 4.2 1.6 - - - +
71A GLU 4.7 0.2 - - - +
75A LYS* 1.3 80.5 - - - +
77A GLY* 1.3 58.3 + - - +
206A ALA* 3.7 7.2 - - - -
207A ALA* 3.3 26.7 - - - +
210A PHE* 3.2 21.3 - - - -
257A GLN* 3.4 5.1 - - - +
258A LEU 2.9 32.3 + - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.3 10.4 - - - +
68A TYR* 3.1 42.5 + - - -
69A SER* 3.1 15.0 + - - -
76A SER* 1.3 76.1 + - - +
78A LEU* 1.3 59.7 + - - -
210A PHE* 3.8 2.9 - - - -
256A TYR 3.5 5.6 - - - -
257A GLN* 4.1 8.3 - - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.4 46.7 - - + +
66A ARG* 3.3 42.0 - - - +
67A VAL* 3.7 8.5 - - + +
68A TYR* 3.4 4.1 - - - -
77A GLY* 1.3 75.0 - - - +
79A ALA* 1.3 64.6 + - - +
80A TRP* 3.8 2.8 - - + -
196A PHE* 3.8 24.5 - - + -
210A PHE* 3.7 22.7 - - + -
255A ASP* 3.7 0.3 - - - -
256A TYR* 2.6 46.7 + - + +
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Residues in contact with ALA 79 (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 GLN 3.6 5.1 - - - +
65A TYR* 3.4 3.6 - - - -
66A ARG* 3.0 35.2 + - + +
68A TYR* 3.6 13.2 - - + -
78A LEU* 1.3 75.7 - - - +
80A TRP* 1.3 59.0 + - - +
253A ARG* 3.9 21.8 - - - +
254A ASP 3.4 6.1 - - - -
274A TRP* 3.5 26.0 - - + -
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN 4.9 0.2 - - - -
65A TYR* 3.9 20.6 - - + +
78A LEU* 3.8 13.0 - - + -
79A ALA* 1.3 75.4 - - - +
81A PRO* 1.3 88.7 - - + +
82A SER* 3.3 14.1 + - - -
171A PHE* 3.5 34.8 - + - -
184A ARG* 3.6 29.6 - - + -
195A LEU* 3.9 12.8 - - + -
196A PHE* 3.4 22.7 - + + -
220A LEU* 3.6 11.0 - - + -
253A ARG* 3.1 8.7 - - - +
254A ASP* 2.8 60.4 + - + +
256A TYR* 3.8 7.1 - - + +
269A ASN* 3.0 23.5 + - - -
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Residues in contact with PRO 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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63A GLY 3.3 19.5 - - - +
65A TYR 4.4 1.3 - - - +
80A TRP* 1.3 96.1 - - + +
82A SER* 1.3 63.1 + - - +
83A ALA 3.3 1.8 - - - +
84A PHE* 3.6 29.2 - - + -
153A PHE* 3.8 8.5 - - - -
220A LEU* 3.3 49.2 - - + +
251A ARG* 4.2 10.1 - - + -
252A VAL 3.4 8.1 - - - +
253A ARG* 4.1 2.9 - - + -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 3.3 20.0 + - - -
81A PRO* 1.3 73.4 - - - +
83A ALA* 1.3 60.6 + - - +
153A PHE* 4.6 1.1 - - - -
170A ILE* 3.5 2.4 - - - +
171A PHE* 2.8 29.3 + - - +
184A ARG* 3.7 17.7 + - - -
252A VAL* 2.8 21.7 + - - +
254A ASP* 2.7 38.0 + - - -
272A ASP* 3.9 0.3 + - - -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 3.3 1.9 - - - +
82A SER* 1.3 83.3 - - - +
84A PHE* 1.3 66.5 + - - +
85A LYS* 4.6 12.1 - - + -
169A VAL 3.4 7.0 - - - -
170A ILE* 4.1 18.6 - - + -
251A ARG* 3.5 4.5 - - - +
252A VAL* 2.8 51.3 + - + +
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Residues in contact with PHE 84 (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 ILE* 3.7 44.0 - - + -
62A ALA 3.9 11.9 - - - -
81A PRO* 3.6 23.3 - - + -
83A ALA* 1.3 76.3 - - - +
85A LYS* 1.3 62.9 + - - +
153A PHE* 3.8 27.1 - + - -
168A LYS* 3.3 3.5 - - - -
169A VAL* 2.8 47.7 + - + +
219A LEU* 3.3 28.9 - - + -
224A PHE* 3.8 41.3 - + + -
250A GLU 3.5 4.7 - - - +
251A ARG* 4.7 1.8 - - + -
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Residues in contact with LYS 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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61A ILE* 4.0 3.2 - - - +
83A ALA* 4.6 8.7 - - + -
84A PHE* 1.3 80.9 - - - +
86A VAL* 1.3 69.0 + - - +
87A GLN* 4.3 17.3 - - + +
158A GLU* 4.3 15.2 + - - +
167A TRP 3.3 6.7 - - - +
168A LYS* 3.9 24.1 - - + +
170A ILE* 5.9 0.2 - - - -
228A PHE* 6.2 0.2 - - - -
248A ILE 4.3 0.7 - - - -
249A TYR* 3.4 1.9 - - - -
250A GLU* 2.9 64.9 + - + +
252A VAL* 4.3 18.3 - - + +
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Residues in contact with VAL 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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57A THR* 3.6 33.9 - - + +
61A ILE* 4.7 2.5 - - + -
84A PHE 5.9 0.2 - - - -
85A LYS* 1.3 80.9 - - - +
87A GLN* 1.3 65.3 + - - +
88A LEU* 4.4 8.1 - - + -
166A GLY* 3.1 2.8 - - - -
167A TRP* 2.9 32.6 + - + -
224A PHE* 5.5 1.1 - - + -
226A PRO* 3.7 30.7 - - + -
228A PHE* 3.7 22.6 - - + -
247A VAL* 5.0 0.2 - - + -
248A ILE 3.3 4.5 - - - +
249A TYR* 4.0 22.0 - - + -
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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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85A LYS* 4.3 25.3 - - + +
86A VAL* 1.3 86.7 - - - +
88A LEU* 1.3 67.2 + - - +
89A GLN* 6.2 0.7 - - + -
158A GLU* 4.3 11.1 + - - -
164A LYS* 6.5 0.7 - - - -
165A VAL 3.4 9.4 - - - +
166A GLY* 4.4 6.8 - - - -
167A TRP 5.1 0.9 - - - +
247A VAL* 3.3 4.7 - - - +
248A ILE* 2.8 62.7 + - + +
250A GLU* 5.1 6.5 + - + +
277A ARG* 4.6 11.6 + - - -
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Residues in contact with LEU 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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55A ILE* 3.9 28.5 - - + -
57A THR* 4.1 18.6 - - + -
86A VAL* 4.4 3.4 - - + -
87A GLN* 1.3 82.4 - - - +
89A GLN* 1.3 61.7 + - - +
98A ILE* 4.2 2.3 - - + +
163A LYS 4.0 0.4 - - - +
164A LYS* 3.3 3.3 - - - +
165A VAL* 2.9 42.6 + - + +
167A TRP* 3.8 20.4 - - + -
230A THR* 3.5 32.8 - - + +
245A ILE* 4.2 18.4 - - + -
246A ASP 3.3 4.9 - - - +
247A VAL* 4.2 14.6 - - + -
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Residues in contact with GLN 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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87A GLN* 6.2 1.1 - - + -
88A LEU* 1.3 77.7 - - - +
90A LEU* 1.3 72.7 + - - +
91A PRO* 3.8 3.9 - - + +
163A LYS* 3.3 8.4 - - - +
164A LYS* 4.1 34.6 - - + +
245A ILE* 3.6 7.0 - - - +
246A ASP* 2.8 49.3 + - + +
248A ILE* 5.0 9.4 - - + +
277A ARG* 5.6 3.3 + - - -
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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