Contacts of the helix formed by residues 88 - 106 (chain A) in PDB entry 4Y1W
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A THR 4.5 1.4 + - - -
85A SER 4.3 5.3 + - - -
86A THR 3.5 3.4 - - - -
87A TRP* 1.3 74.7 - - - +
89A VAL* 1.3 63.8 + - - -
91A GLY* 3.0 12.1 + - - -
92A ALA* 3.5 7.8 + - - +
95A ARG* 5.1 1.7 + - - -
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Residues in contact with VAL 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 TRP 3.3 0.8 + - - +
88A GLY* 1.3 72.1 - - - -
90A ALA* 1.3 61.1 + - + +
92A ALA* 3.3 10.2 + - + +
93A ASP* 2.9 37.5 + - - +
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Residues in contact with ALA 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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74A THR* 5.5 2.9 - - + +
87A TRP* 3.0 31.5 + - + +
89A VAL* 1.3 85.2 - - + +
91A GLY* 1.3 53.7 + - - +
93A ASP* 3.8 8.3 - - - +
94A ALA* 2.8 29.5 + - - +
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Residues in contact with GLY 91 (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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78A TYR* 4.1 7.3 - - - -
84A THR* 5.8 0.2 - - - -
87A TRP* 3.6 25.2 - - - +
88A GLY 3.0 9.8 + - - -
90A ALA* 1.3 76.0 - - - +
92A ALA* 1.3 59.3 + - - +
94A ALA* 3.3 2.3 + - - +
95A ARG* 2.9 47.7 + - - +
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Residues in contact with ALA 92 (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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88A GLY 3.5 3.9 + - - +
89A VAL* 3.3 16.0 + - + +
91A GLY* 1.3 76.4 - - - +
93A ASP* 1.3 63.3 + - - +
95A ARG* 3.4 26.6 + - - +
96A GLN* 3.1 23.0 + - - +
99A ARG* 5.1 0.9 + - - -
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Residues in contact with ASP 93 (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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89A VAL* 2.9 24.9 + - - +
90A ALA* 3.8 8.2 - - - +
92A ALA* 1.3 78.1 - - - +
94A ALA* 1.3 57.5 + - - +
96A GLN* 3.3 7.5 + - - +
97A TYR* 2.8 31.0 + - - +
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Residues in contact with ALA 94 (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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74A THR* 4.7 9.9 - - + +
75A ALA* 5.3 2.5 - - - +
78A TYR* 4.0 31.0 - - + -
87A TRP* 4.1 7.9 - - + -
90A ALA 2.8 19.1 + - - +
91A GLY 3.3 4.2 + - - +
93A ASP* 1.3 76.8 - - - +
95A ARG* 1.3 57.7 + - - +
97A TYR* 3.3 6.7 + - - +
98A ILE* 2.9 39.5 + - + +
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Residues in contact with ARG 95 (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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78A TYR* 2.9 45.1 + - + +
84A THR* 5.1 3.4 + - - -
88A GLY 5.1 1.8 + - - -
91A GLY* 2.9 29.3 + - - +
92A ALA* 3.4 29.9 - - - +
94A ALA* 1.3 76.1 - - - +
96A GLN* 1.3 63.3 + - - +
98A ILE* 3.5 7.7 + - - +
99A ARG* 3.0 42.7 + - - +
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Residues in contact with GLN 96 (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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92A ALA 3.1 15.9 + - - +
93A ASP* 3.7 8.3 - - - +
94A ALA 3.3 0.2 - - - -
95A ARG* 1.3 75.8 - - - +
97A TYR* 1.3 58.4 + - - +
99A ARG* 2.5 45.4 + - - +
100A THR* 2.9 47.9 + - - +
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Residues in contact with TYR 97 (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 ALA* 2.7 47.3 + - + -
66A ASP* 3.7 8.0 - - + -
67A PHE* 3.0 30.8 + + - +
71A GLY* 3.7 27.4 - - - -
75A ALA* 4.1 17.9 - - + -
93A ASP 2.8 17.5 + - - +
94A ALA* 3.7 6.7 - - - +
96A GLN* 1.3 78.8 - - - +
98A ILE* 1.3 63.6 + - - +
100A THR* 3.2 6.6 + - - -
101A VAL* 2.9 36.9 + - + +
140A PHE* 5.8 0.4 - + - -
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Residues in contact with ILE 98 (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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75A ALA* 4.0 26.2 - - + +
78A TYR* 3.7 33.2 - - + -
79A LEU* 3.9 20.6 - - + -
94A ALA 2.9 22.8 + - - +
95A ARG* 3.8 5.8 - - - +
97A TYR* 1.3 77.5 - - - +
99A ARG* 1.3 62.7 + - - +
101A VAL* 3.4 1.4 + - - +
102A LYS* 3.0 44.8 + - + +
140A PHE* 4.1 19.0 - - + -
196A PRO* 4.5 7.0 - - + -
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Residues in contact with ARG 99 (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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92A ALA 5.1 1.0 + - - -
95A ARG* 3.0 41.3 + - - +
96A GLN* 2.5 43.8 + - - +
98A ILE* 1.3 76.8 - - - +
100A THR* 1.3 58.1 + - - +
102A LYS* 3.4 8.9 + - - +
103A SER* 3.0 30.0 + - - -
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Residues in contact with THR 100 (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 ASN* 3.8 10.9 - - + +
60A GLU* 3.8 25.3 - - + +
63A ALA* 3.7 24.7 - - + -
96A GLN* 2.9 35.6 + - - +
97A TYR* 3.6 6.7 - - - -
99A ARG* 1.3 75.6 - - - +
101A VAL* 1.3 59.5 + - - +
103A SER* 3.3 6.8 + - - -
104A ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 101 (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 ALA* 4.0 13.7 - - + +
64A VAL* 4.7 9.6 - - + +
67A PHE* 4.2 14.8 - - + -
97A TYR* 2.9 56.2 + - + +
98A ILE 3.9 2.7 - - - +
100A THR* 1.3 74.6 - - - +
102A LYS* 1.3 58.2 + - - +
104A ALA* 3.2 7.3 + - - +
105A LEU* 2.9 30.7 + - + +
140A PHE* 3.7 27.1 - - + -
193A LEU* 4.3 12.3 - - + -
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Residues in contact with LYS 102 (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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98A ILE* 3.0 39.7 + - + +
99A ARG* 3.7 7.8 - - - +
101A VAL* 1.3 75.2 - - - +
103A SER* 1.3 63.8 - - - +
105A LEU* 3.3 18.3 + - - +
106A ASN* 3.4 19.5 + - - +
140A PHE* 4.1 6.3 - - + -
195A ALA* 4.3 11.2 - - + -
196A PRO* 3.9 29.5 - - + +
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Residues in contact with SER 103 (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 GLU* 2.4 26.9 + - - -
99A ARG* 3.0 18.5 + - - -
100A THR* 3.6 5.6 - - - -
102A LYS* 1.3 78.5 - - - +
104A ALA* 1.3 62.1 + - - +
106A ASN* 3.4 14.7 + - - +
107A LYS* 3.7 22.2 + - - +
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Residues in contact with ALA 104 (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 ILE* 4.5 9.3 - - + +
60A GLU* 3.8 28.0 + - + +
64A VAL* 3.5 26.7 - - + -
100A THR 2.9 17.0 + - - +
101A VAL 3.5 5.6 - - - +
103A SER* 1.3 77.8 + - - +
105A LEU* 1.3 62.4 + - - +
107A LYS* 2.9 16.3 + - - +
108A LEU* 3.4 15.3 + - - +
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Residues in contact with LEU 105 (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 VAL* 5.8 1.1 - - + -
101A VAL* 2.9 19.3 + - + +
102A LYS* 3.3 10.2 + - - +
104A ALA* 1.3 75.6 - - - +
106A ASN* 1.3 62.2 + - - +
108A LEU* 3.1 12.5 + - + +
140A PHE* 4.4 7.6 - - + -
178A HIS* 2.9 51.0 + - + -
180A ILE* 3.8 29.2 - - + -
193A LEU* 3.9 26.9 - - + +
194A PHE 4.0 6.1 - - - -
195A ALA* 3.8 34.5 - - + +
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Residues in contact with ASN 106 (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 ARG* 3.7 19.8 + - - -
102A LYS* 3.4 14.7 + - - +
103A SER* 3.8 10.1 - - - +
104A ALA 3.2 1.0 - - - -
105A LEU* 1.3 81.1 - - - +
107A LYS* 1.3 61.0 + - + +
108A LEU 3.5 2.3 + - - +
178A HIS* 4.1 18.5 + - - -
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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