Contacts of the strand formed by residues 56 - 70 (chain A) in PDB entry 5I2S
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 1.3 75.3 - - - +
57A TRP* 1.3 72.8 + - - -
131A PRO* 3.4 5.2 - - - +
132A HIS 2.8 38.6 + - - -
133A HIS* 4.3 0.8 - - - -
167A TRP* 3.4 9.0 - - - -
168A HIS 3.2 13.2 - - - -
170A ASP* 3.9 2.4 - - - +
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Residues in contact with TRP 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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55A ASP* 5.9 1.1 - - + +
56A GLY* 1.3 80.5 - - - +
58A MET* 1.3 61.5 + - - +
96A ILE* 3.4 45.3 - - + +
99A THR* 4.2 24.9 - - + -
100A LYS* 3.7 31.0 - - + -
129A VAL* 4.1 19.7 - - + -
130A THR 3.5 7.4 - - - -
131A PRO* 3.5 42.8 - - + -
132A HIS 4.4 0.2 - - - +
166A THR 3.6 0.9 - - - +
167A TRP* 3.4 5.9 - - - +
168A HIS* 2.8 40.1 + - + +
169A SER 5.2 0.2 - - - -
170A ASP* 3.2 34.2 + - + +
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 1.3 72.9 - - - +
59A CYS* 1.3 58.4 + - - +
60A HIS* 4.2 3.8 + - - +
128A GLN 3.8 1.0 - - - +
129A VAL* 3.2 4.1 - - - -
130A THR* 2.9 44.0 + - - +
132A HIS* 3.5 38.6 - - + +
147A GLN* 3.3 31.2 - - - +
148A PHE* 5.3 1.1 - - - -
160A THR* 3.4 20.2 - - + +
165A THR* 3.4 26.7 - - + -
166A THR 3.5 6.3 - - - -
167A TRP* 3.5 31.2 - - - -
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Residues in contact with CYS 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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57A TRP 4.8 0.9 - - - +
58A MET* 1.3 73.3 - - - +
60A HIS* 1.3 63.4 + - - +
87A PRO* 3.9 3.5 - - - +
92A CYS* 2.0 57.9 - - + -
127A VAL* 3.8 16.8 - - - -
128A GLN 3.4 4.0 - - - -
129A VAL* 3.6 13.5 - - + -
164A SER 3.7 0.9 - - - +
165A THR* 3.4 2.7 - - - +
166A THR* 2.8 43.5 + - + +
168A HIS* 4.1 6.3 - - + -
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 4.2 5.8 + - - +
59A CYS* 1.3 76.9 - - - +
61A ALA* 1.3 62.9 + - - +
87A PRO* 4.5 2.0 - - - -
126A ILE 4.2 0.2 - - - +
127A VAL* 3.5 4.7 - - - +
128A GLN* 2.9 79.0 + - + +
130A THR* 4.2 21.7 + - + -
164A SER* 4.0 14.4 - - - +
165A THR* 4.0 15.9 - - + +
408A PRO* 3.4 44.5 + - + +
409A HIS* 4.1 13.6 + + + -
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Residues in contact with ALA 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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60A HIS* 1.3 80.4 - - - +
62A SER* 1.3 63.5 + - - +
84A SER* 3.4 8.1 + - - -
85A PHE* 2.8 53.2 + - + +
87A PRO* 3.5 27.2 - - + +
126A ILE 3.5 3.8 - - - -
127A VAL* 4.0 11.2 - - + -
164A SER* 4.6 1.9 + - - -
409A HIS* 5.1 1.6 - - - -
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Residues in contact with SER 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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61A ALA* 1.3 76.2 - - - +
63A LYS* 1.3 59.0 + - - +
64A TRP* 3.2 27.2 + - - -
82A ILE* 3.9 7.9 - - - -
83A ARG 3.9 0.2 - - - -
84A SER* 3.8 9.2 - - - +
85A PHE* 4.1 5.7 - - - +
125A VAL* 3.7 1.4 - - - -
126A ILE* 2.9 36.5 + - - +
128A GLN* 4.2 5.7 + - - -
409A HIS* 3.8 32.7 - - - +
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Residues in contact with LYS 63 (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 SER* 1.3 69.6 - - - +
64A TRP* 1.3 63.1 + - - +
65A VAL* 3.8 6.8 - - + +
82A ILE* 3.6 2.3 - - - -
83A ARG* 2.9 52.2 + - + +
85A PHE* 3.9 26.7 - - + +
123A GLU* 3.2 34.8 + - - +
124A ALA 3.8 2.9 - - - +
125A VAL* 3.5 26.5 - - + -
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Residues in contact with TRP 64 (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 SER* 3.2 31.0 + - - -
63A LYS* 1.3 78.0 - - - +
65A VAL* 1.3 60.3 + - - +
66A THR 4.1 0.4 - - - -
81A SER 4.0 3.1 - - - -
82A ILE* 3.5 25.4 - - + +
106A ASN* 3.9 24.7 - - - -
108A GLY* 3.9 28.9 - - - +
109A PHE* 3.8 38.6 - + + -
110A PRO* 3.7 6.7 - - + +
123A GLU* 3.0 23.6 - - - -
124A ALA 2.9 18.3 + - - +
126A ILE* 3.5 21.7 - - + +
128A GLN* 5.5 1.8 - - - -
409A HIS* 4.9 16.1 + - + -
412A ASP* 5.9 4.3 - - + -
413A ALA* 5.3 14.6 - - + -
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Residues in contact with VAL 65 (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 LYS* 3.8 12.8 - - + +
64A TRP* 1.3 75.3 - - - +
66A THR* 1.3 61.6 + - - +
67A THR* 3.8 7.0 + - - +
79A THR 3.9 0.7 - - - +
80A HIS* 3.4 5.9 - - - -
81A SER* 2.9 56.8 + - - +
83A ARG* 4.2 23.3 - - - +
109A PHE* 4.2 4.7 - - - -
121A ASP* 3.7 38.8 - - + +
122A ALA 3.5 4.5 - - - +
123A GLU* 4.3 16.8 - - + +
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Residues in contact with THR 66 (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 TRP 4.1 0.6 + - - -
65A VAL* 1.3 70.8 - - - +
67A THR* 1.3 62.8 + - - +
68A CYS 4.3 0.4 + - - +
78A ILE* 4.4 6.3 - - + -
80A HIS* 3.3 25.5 + - + +
109A PHE* 3.4 19.6 - - - +
110A PRO* 3.1 24.1 + - - +
111A PRO 4.4 3.8 - - - -
112A GLN* 3.8 31.9 - - + -
113A SER 5.1 1.8 + - - +
120A THR 4.2 1.2 - - - +
121A ASP* 3.8 1.9 - - - +
122A ALA* 2.8 39.2 + - - +
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Residues in contact with THR 67 (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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65A VAL* 3.8 10.6 + - - +
66A THR* 1.3 73.0 - - - +
68A CYS* 1.3 63.5 + - - +
69A ASP* 4.8 2.9 - - + +
77A TYR 3.8 1.5 - - - +
78A ILE* 3.1 10.4 - - - +
79A THR* 2.9 52.6 + - - +
81A SER* 5.0 3.8 + - - -
83A ARG* 5.7 1.7 + - - -
119A VAL* 3.6 24.7 - - + -
120A THR 4.2 1.3 - - - +
121A ASP* 3.0 25.3 + - - +
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Residues in contact with CYS 68 (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 THR 4.3 0.2 - - - -
67A THR* 1.3 74.2 - - - +
69A ASP* 1.3 61.5 + - - +
70A PHE* 3.3 10.3 + - - +
76A LYS* 3.6 23.6 - - - -
77A TYR 4.1 1.6 - - - -
78A ILE* 4.5 9.9 - - + -
112A GLN* 5.1 4.0 - - + -
113A SER 3.6 17.7 - - - +
114A CYS* 2.0 51.2 - - + -
118A THR 4.1 2.6 - - - +
119A VAL* 3.8 18.1 - - - -
120A THR* 3.7 9.9 + - - -
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Residues in contact with ASP 69 (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 THR* 3.9 2.8 - - + -
68A CYS* 1.3 69.8 - - - +
70A PHE* 1.3 62.0 + - - +
71A ARG* 3.2 47.3 + - - +
75A PRO 3.9 1.0 - - - +
76A LYS* 3.4 4.7 - - - -
77A TYR* 2.9 49.3 + - + +
119A VAL* 3.2 31.8 - - + +
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Residues in contact with PHE 70 (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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68A CYS* 3.3 10.7 + - - +
69A ASP* 1.3 73.5 + - - +
71A ARG* 1.3 75.1 + - - +
72A TRP 4.0 0.2 + - - -
74A GLY* 3.5 23.3 - - - -
76A LYS* 3.4 43.7 - - + +
114A CYS* 4.4 11.4 - - + -
115A GLY 3.8 9.6 - - - +
116A TYR* 3.1 55.4 - + - +
117A ALA* 4.4 9.2 - - - +
118A THR 4.5 4.8 + - - +
119A VAL* 5.0 0.6 - - - +
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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
------------------------------------------------------------
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