Contacts of the strand formed by residues 92 - 102 (chain I) in PDB entry 1CEW
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 TYR 92 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45I VAL* 3.6 36.4 - - + +
65I GLU* 3.8 28.7 - - - +
66I ILE 3.3 10.3 - - - +
67I GLY* 4.1 5.2 - - - -
88I GLU 4.9 9.8 + - - -
89I MET 6.2 0.7 - - - -
90I ALA 5.9 0.7 - - - -
91I LYS* 1.3 98.0 - - - +
93I THR* 1.3 59.4 + - - +
116I GLN 5.6 0.3 - - - +
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Residues in contact with THR 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I TYR* 3.8 17.4 + - - +
65I GLU* 3.3 3.1 - - - +
66I ILE* 2.7 40.4 + - + +
91I LYS* 4.5 9.5 + - - +
92I TYR* 1.3 74.3 + - - +
94I THR* 1.3 68.7 + - - +
95I CYS* 3.6 25.6 - - - -
115I CYS* 4.1 9.4 - - + -
116I GLN* 4.5 13.9 + - - +
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Residues in contact with THR 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ILE* 3.5 29.5 - - + +
63I GLN* 4.6 6.1 - - - +
64I VAL 3.3 3.4 - - - +
65I GLU* 4.1 19.9 + - - +
93I THR* 1.3 78.4 + - - +
95I CYS* 1.4 66.8 + - - +
115I CYS* 3.6 1.6 - - - -
116I GLN* 3.2 47.2 + - + +
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Residues in contact with CYS 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TYR* 4.0 3.8 - - - -
62I LEU 3.9 0.2 - - - +
63I GLN* 3.2 4.3 - - - +
64I VAL 2.7 39.6 + - - +
66I ILE* 3.3 31.6 - - + -
93I THR* 3.6 9.0 - - - -
94I THR* 1.4 73.3 - - - +
96I THR* 1.3 61.0 + - - +
97I PHE* 4.0 19.0 + - + -
114I LYS 3.5 4.9 - - - -
115I CYS* 2.0 47.3 - - - -
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Residues in contact with THR 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ILE* 4.2 18.8 - - + -
62I LEU 3.3 11.2 - - - +
63I GLN* 4.0 17.3 + - + +
95I CYS* 1.3 75.4 + - - +
97I PHE* 1.3 65.6 + - - +
98I VAL* 4.5 7.9 - - + -
112I GLU* 3.7 10.5 - - - +
113I SER* 3.3 3.5 - - - -
114I LYS* 3.0 46.5 + - - -
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Residues in contact with PHE 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU* 5.1 1.8 - - + -
28I ALA* 3.5 28.5 - - + -
29I MET* 3.2 36.6 - - + -
32I TYR* 4.3 13.0 - + + -
60I TYR 3.7 0.5 - - - +
61I ILE* 3.4 2.3 - - - +
62I LEU* 2.8 56.2 + - + +
64I VAL* 4.4 14.4 - - + -
66I ILE* 4.1 3.8 - - + -
95I CYS* 4.0 22.4 - - + -
96I THR* 1.3 76.4 - - - +
98I VAL* 1.3 63.0 + - - +
99I VAL 3.9 0.2 - - - -
110I LEU* 4.1 18.8 - - + -
112I GLU 3.5 1.8 - - - -
113I SER* 3.3 29.4 - - - -
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Residues in contact with VAL 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I LYS* 4.2 26.9 - - + -
60I TYR 3.1 10.1 - - - +
61I ILE* 4.1 20.2 - - + -
96I THR* 4.5 4.3 - - + -
97I PHE* 1.3 78.7 - - - +
99I VAL* 1.4 59.3 + - - +
110I LEU* 3.8 3.3 - - - +
111I LEU* 3.2 40.7 + - + -
112I GLU* 3.0 40.4 + - + +
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Residues in contact with VAL 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ALA* 3.7 15.7 - - + +
27I PHE* 3.5 24.2 - - + -
28I ALA* 4.6 0.7 - - + -
58I ILE 3.9 0.6 - - - +
59I LYS* 3.3 4.5 - - - +
60I TYR* 2.8 41.3 + - + +
62I LEU* 3.5 27.6 - - + -
97I PHE* 4.5 0.4 - - + -
98I VAL* 1.4 74.5 - - - +
100I TYR* 1.3 59.1 + - - +
101I SER* 6.1 0.4 - - - -
108I ILE* 3.7 17.3 - - + -
109I LYS 3.0 18.2 - - - +
110I LEU* 3.5 17.7 - - + -
111I LEU* 5.2 0.2 - - - -
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Residues in contact with TYR 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I VAL* 3.7 26.4 - - + +
56I SER* 3.0 23.9 + - - -
57I GLY* 3.7 19.2 + - - -
58I ILE 3.5 8.3 - - - -
59I LYS* 4.1 12.6 - - + -
99I VAL* 1.3 74.6 - - - +
101I SER* 1.3 61.0 + - - +
102I ILE* 3.8 31.0 + - + +
104I TRP* 5.3 0.5 - - - -
107I GLN 4.2 0.5 - - - +
108I ILE* 3.4 1.6 - - - -
109I LYS* 2.7 40.0 + - + +
111I LEU* 3.5 37.4 - - + +
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Residues in contact with SER 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ARG* 3.1 29.6 + - - -
57I GLY* 3.0 8.1 - - - -
58I ILE* 2.8 48.2 + - - +
60I TYR* 4.4 14.1 - - - -
99I VAL 5.8 0.2 - - - -
100I TYR* 1.3 73.5 - - - +
102I ILE* 1.3 62.5 + - - +
103I PRO* 3.2 7.2 - - - +
107I GLN 3.5 8.3 + - - -
108I ILE* 4.3 6.8 - - - +
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Residues in contact with ILE 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I GLY* 4.6 2.0 - - - -
100I TYR* 3.8 34.3 - - + +
101I SER* 1.3 77.6 + - - +
103I PRO* 1.3 57.4 - - - +
104I TRP* 3.0 46.7 + - + +
105I LEU* 3.1 22.6 + - + -
107I GLN* 2.6 52.3 + - + +
109I LYS* 4.8 6.7 - - + -
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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
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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