Contacts of the helix formed by residues 91 - 110 (chain A) in PDB entry 5PSY
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 ASN 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.7 12.6 - - - -
39A LEU* 4.5 0.6 - - - +
89A TYR* 3.3 8.3 - - - +
90A LYS* 1.3 84.9 - - - +
92A LEU* 1.3 63.0 + - - +
93A HIS* 3.2 13.4 + - + +
94A GLU* 2.9 52.7 + - - +
95A PHE* 3.7 7.4 + - - +
135A ARG* 6.2 0.2 - - - +
138A VAL* 6.2 1.1 - - + -
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Residues in contact with LEU 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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35A LEU* 4.6 4.9 - - - +
39A LEU* 3.7 26.0 - - + -
42A VAL* 5.5 0.7 - - + -
91A ASN* 1.3 72.7 - - - +
93A HIS* 1.3 60.0 + - - +
95A PHE* 3.2 12.6 + - + -
96A GLU* 2.8 51.8 + - + +
131A LEU* 4.5 9.2 - - + +
134A ALA* 4.0 12.3 - - + +
135A ARG* 3.6 61.0 - - + +
138A VAL* 4.5 17.4 - - + +
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.2 13.9 + - - +
92A LEU* 1.3 78.2 - - - +
94A GLU* 1.3 61.2 + - + +
96A GLU* 3.3 16.9 + - + +
97A GLU* 2.9 65.3 + - + +
135A ARG* 4.1 10.6 - - - +
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Residues in contact with GLU 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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83A ARG* 3.2 24.4 + - - +
88A GLY 3.6 1.7 - - - +
89A TYR* 3.7 17.7 - - + -
90A LYS* 2.9 37.5 + - - +
91A ASN* 2.9 31.1 + - - +
92A LEU 3.3 0.2 - - - -
93A HIS* 1.3 77.8 - - + +
95A PHE* 1.3 62.0 + - - +
97A GLU* 3.4 15.6 + - - +
98A ASP* 3.3 17.8 + - - +
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Residues in contact with PHE 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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39A LEU* 3.8 47.6 - - + -
42A VAL* 3.7 25.1 - - + -
43A LEU* 3.9 24.9 - - + -
46A LEU* 3.9 13.2 - - + -
80A MET* 3.6 28.3 - - + +
84A LEU* 5.0 2.2 - - + -
89A TYR* 3.5 35.5 - + + -
91A ASN 3.7 2.3 + - - +
92A LEU* 3.2 21.2 + - + +
94A GLU* 1.3 75.1 - - - +
96A GLU* 1.3 70.9 + - - +
98A ASP* 3.1 4.3 + - - -
99A PHE* 3.0 20.0 + - + +
131A LEU* 4.4 4.0 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 2.8 37.8 + - + +
93A HIS* 3.7 18.5 + - + +
95A PHE* 1.3 78.2 - - - +
97A GLU* 1.3 56.4 + - - +
99A PHE* 3.6 8.2 - - + +
100A ASP* 2.8 41.9 + - - +
131A LEU* 3.9 42.7 - - + +
135A ARG* 4.5 8.2 + - - +
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Residues in contact with GLU 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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93A HIS* 2.9 52.1 + - + +
94A GLU* 3.4 14.9 - - - +
95A PHE 3.2 0.2 - - - -
96A GLU* 1.3 75.6 - - - +
98A ASP* 1.3 60.7 + - - +
100A ASP* 3.4 7.7 + - - +
101A LEU* 3.0 32.4 + - + +
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Residues in contact with ASP 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 MET* 3.4 40.4 - - + +
80A MET* 3.9 12.1 - - + -
83A ARG* 3.5 17.3 + - - -
89A TYR* 2.6 38.7 + - - +
94A GLU 3.3 3.8 + - - +
95A PHE 3.1 8.0 + - - +
97A GLU* 1.3 79.4 - - - +
99A PHE* 1.3 65.2 + - - +
101A LEU* 3.2 19.8 + - - +
102A ILE* 3.3 9.7 + - - +
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Residues in contact with PHE 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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46A LEU* 3.8 36.3 - - + -
77A PHE* 4.3 13.7 - + - -
80A MET* 3.8 12.8 - - + -
95A PHE* 3.0 13.1 + - + +
96A GLU* 3.2 10.3 + - - +
98A ASP* 1.3 73.6 - - - +
100A ASP* 1.3 74.5 + - - +
102A ILE* 3.1 18.3 + - + +
103A ILE* 3.3 21.7 + - + +
123A LEU* 3.8 51.6 - - + -
124A ARG* 4.8 6.7 - - + -
127A GLY* 4.7 3.6 - - - -
128A GLY 5.4 0.2 - - - -
131A LEU* 3.7 30.3 - - + -
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Residues in contact with ASP 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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96A GLU* 2.8 27.4 + - - +
97A GLU* 3.6 7.7 - - - +
99A PHE* 1.3 90.0 - - - +
101A LEU* 1.3 51.8 + - - +
103A ILE* 3.3 6.8 + - - +
104A ASP* 2.8 52.0 + - - +
124A ARG* 5.9 2.8 - - - +
131A LEU* 5.6 1.7 - - - +
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Residues in contact with LEU 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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73A HIS* 3.6 39.3 - - + +
75A MET* 3.7 18.4 - - + -
97A GLU* 3.0 16.1 + - + +
98A ASP* 3.2 27.8 + - - +
100A ASP* 1.3 73.2 - - - +
102A ILE* 1.3 67.7 + - - +
104A ASP* 4.4 4.7 - - + +
105A ASN* 2.9 43.2 + - - +
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Residues in contact with ILE 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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55A PHE* 3.4 38.9 - - + -
75A MET* 3.8 12.3 - - + +
76A ASP 3.6 42.6 - - - +
77A PHE* 3.7 20.2 - - + +
80A MET* 3.7 24.2 - - - -
98A ASP 3.3 9.1 + - - +
99A PHE* 3.1 12.3 + - + +
101A LEU* 1.3 82.4 - - - +
103A ILE* 1.3 67.4 + - + +
105A ASN* 4.1 2.2 - - - +
106A CYS* 3.4 20.6 + - - +
123A LEU* 4.6 3.8 - - + -
202A EDO 5.4 1.4 - - - -
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Residues in contact with ILE 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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55A PHE* 5.1 0.9 - - + -
99A PHE* 3.7 24.0 - - + +
100A ASP* 3.3 9.4 + - - +
101A LEU 3.2 0.4 - - - -
102A ILE* 1.3 78.7 - - + +
104A ASP* 1.3 75.1 + - - +
106A CYS* 3.3 4.0 + - - +
107A MET* 3.0 46.5 + - - +
120A ALA* 3.5 28.0 - - + +
123A LEU* 3.5 34.5 - - + -
124A ARG* 4.0 29.2 - - + +
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Residues in contact with ASP 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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100A ASP* 2.8 36.8 + - - +
101A LEU* 4.4 5.2 - - + +
103A ILE* 1.3 84.3 - - - +
105A ASN* 1.3 63.9 + - - +
107A MET* 3.4 7.9 + - - +
108A LYS* 3.2 48.0 + - - +
124A ARG* 5.9 0.9 - - - -
108B LYS* 6.2 0.2 - - - +
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Residues in contact with ASN 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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67A TYR* 3.9 16.0 + - - +
71A ILE* 3.4 38.7 - - + +
73A HIS 2.8 27.7 + - - +
74A PRO* 3.5 8.5 - - - +
75A MET 3.7 8.6 + - - +
101A LEU* 2.9 36.1 + - - +
102A ILE 4.1 2.9 - - - +
104A ASP* 1.3 77.4 - - - +
106A CYS* 1.3 64.3 + - - +
108A LYS* 3.2 3.1 + - - +
109A TYR* 3.0 21.3 + - - +
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Residues in contact with CYS 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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55A PHE* 3.7 15.3 - - + -
67A TYR* 5.0 1.3 + - - -
102A ILE 3.4 12.6 + - - +
103A ILE 3.3 8.7 + - - +
104A ASP 3.3 0.2 - - - -
105A ASN* 1.3 81.4 - - - +
107A MET* 1.3 57.2 + - - +
109A TYR* 4.7 1.3 - - - +
110A ASN* 2.9 44.7 + - - +
116A PHE 3.2 30.7 - - - -
117A TYR* 4.1 0.8 - - - -
120A ALA* 3.8 7.0 - - + -
201A EDO 5.3 0.2 - - - -
202A EDO 3.3 31.2 - - - -
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Residues in contact with MET 107 (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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103A ILE* 3.0 37.5 + - - +
104A ASP* 3.9 9.0 - - - +
105A ASN 3.4 0.2 - - - -
106A CYS* 1.3 76.5 - - - +
108A LYS* 1.3 60.3 + - - +
110A ASN 3.5 10.0 - - - +
117A TYR* 3.4 52.4 - - + +
120A ALA* 3.8 16.6 - - + -
121A VAL* 3.6 21.5 - - + -
124A ARG* 3.8 17.9 - - - +
108B LYS* 3.6 42.3 - - + +
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Residues in contact with LYS 108 (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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71A ILE* 4.5 13.5 - - + -
104A ASP* 3.2 42.5 + - - +
105A ASN* 3.8 4.0 - - - +
106A CYS 3.2 0.2 - - - -
107A MET* 1.3 79.8 - - + +
109A TYR* 1.3 63.6 + - - +
110A ASN 3.3 0.2 - - - -
104B ASP* 3.3 49.3 + - - +
107B MET* 3.3 30.4 - - + +
108B LYS* 3.7 24.5 - - + +
117B TYR* 3.5 9.5 - - - -
201B NA 2.4 26.5 - - - -
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Residues in contact with TYR 109 (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* 2.9 27.1 - - + +
66A ASP* 3.3 8.6 + - - -
67A TYR* 3.8 25.6 - + + +
70A HIS* 3.7 38.6 - + + -
71A ILE* 4.4 4.2 - - + +
105A ASN 3.0 16.4 + - - +
108A LYS* 1.3 77.4 - - - +
110A ASN* 1.3 67.5 + - - +
111A ALA 4.1 0.2 + - - -
201A EDO 3.5 41.5 - - - +
112B ARG* 2.9 74.3 + - - +
117B TYR* 4.5 4.7 - - - -
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Residues in contact with ASN 110 (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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106A CYS* 2.9 31.4 + - - +
107A MET 3.5 9.0 - - - +
108A LYS 4.1 2.8 - - - +
109A TYR* 1.3 86.2 + - - +
111A ALA* 1.3 62.3 + - - +
114A THR* 3.5 19.1 - - - +
116A PHE* 3.6 23.1 - - + +
117A TYR* 3.4 18.2 - - - +
201A EDO 2.9 44.6 + - - -
202A EDO 3.7 0.2 - - - -
108B LYS 5.4 0.3 - - - +
111B ALA* 6.1 0.2 - - - -
112B ARG* 4.4 5.3 - - - +
201B NA 4.2 2.7 - - - -
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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
------------------------------------------------------------
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