Contacts of the strand formed by residues 90 - 97 (chain C) in PDB entry 4DEP
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 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C TRP* 4.5 1.8 - - - -
53C THR 3.6 13.5 - - - -
54C ARG 4.5 0.2 - - - -
55C GLN 4.1 3.6 - - - -
88C ASP 3.2 3.9 + - - -
89C THR* 1.3 74.7 - - - +
91C ASN* 1.3 60.4 + - - -
92C TYR* 3.9 4.7 - - - -
109C LEU* 2.8 34.2 + - - +
403C NAG 3.2 22.2 - - - +
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Residues in contact with ASN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.5 15.3 - - + +
52C TRP* 3.2 4.6 - - - +
53C THR* 3.2 38.6 + - - +
90C GLY* 1.3 70.9 - - - -
92C TYR* 1.3 63.3 + - - +
93C THR* 4.0 0.9 + - - -
106C ALA* 4.7 5.6 - - + -
107C PHE 3.3 5.4 - - - +
108C PRO* 3.0 29.6 - - - +
403C NAG 1.4 65.3 + - - +
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TRP* 5.1 2.5 - - + -
51C TYR 3.6 1.3 - - - +
52C TRP* 3.4 39.4 - + + -
63C ILE* 3.7 27.8 - - + -
72C ILE* 5.2 1.7 - - + +
79C LEU* 3.9 7.6 - - + -
81C PHE* 3.4 27.9 - + - -
88C ASP* 2.6 33.8 + - - +
90C GLY 3.9 4.9 - - - -
91C ASN* 1.3 74.8 - - - +
93C THR* 1.3 60.8 + - - +
94C CYS 4.1 0.2 - - - -
106C ALA* 2.9 4.7 - - - -
107C PHE* 2.8 66.1 + + + -
109C LEU* 3.7 29.8 - - + -
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE 3.7 0.2 - - - +
50C TRP* 3.2 9.7 - - - +
51C TYR* 2.7 86.9 + - + +
91C ASN 4.0 1.7 + - - -
92C TYR* 1.3 71.6 - - - +
94C CYS* 1.3 72.8 + - - +
95C MET* 4.4 0.2 - - + -
104C LYS* 4.3 12.8 - - + +
105C VAL 3.4 7.2 + - - +
106C ALA* 3.0 20.6 - - - +
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Residues in contact with CYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C CYS* 2.1 59.5 - - + -
28C PRO* 4.0 9.0 - - - -
29C LEU* 4.1 4.4 - - - +
48C LEU* 4.0 7.6 - - + -
49C ILE 3.2 7.2 - - - +
50C TRP* 3.8 21.9 - - + -
92C TYR 4.1 1.6 + - - -
93C THR* 1.3 76.0 - - - +
95C MET* 1.3 59.6 + - - +
104C LYS* 3.5 2.3 - - - -
105C VAL* 3.1 34.7 + - - +
107C PHE* 5.2 1.1 - - - -
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Residues in contact with MET 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C CYS* 3.6 9.0 - - + -
29C LEU* 4.6 0.9 - - - -
47C THR 3.6 1.0 - - - +
48C LEU* 3.3 6.8 - - - +
49C ILE* 2.7 70.0 + - + +
51C TYR* 4.4 13.0 - - + +
93C THR* 4.4 5.8 - - + -
94C CYS* 1.3 76.0 - - - +
96C LEU* 1.3 64.3 + - - +
97C ARG* 3.9 21.9 + - - +
102C CYS* 3.6 31.4 - - - -
103C SER 3.5 11.4 - - - +
104C LYS* 3.7 23.3 - - + +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.3 5.3 - - + +
30C PHE* 4.0 21.1 - - + -
34C LEU* 4.0 25.4 - - + -
36C PHE* 4.1 4.7 - - + -
38C TYR* 6.0 1.3 - - + -
41C ALA* 4.2 7.6 - - + -
46C LEU* 3.4 42.4 - - + +
47C THR 3.1 22.2 - - - +
48C LEU* 4.1 17.7 - - + +
95C MET* 1.3 72.1 - - - +
97C ARG* 1.3 60.1 + - - +
101C TYR* 3.9 9.3 - - + -
102C CYS* 3.5 3.3 - - - -
103C SER 2.9 31.6 + - - +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY 4.5 0.3 - - - +
46C LEU* 3.8 5.9 - - - +
47C THR* 2.9 49.6 + - - +
49C ILE* 3.8 27.8 - - + +
95C MET* 3.9 27.5 - - + +
96C LEU* 1.3 76.1 - - - +
98C ASN* 1.3 67.7 + - - +
101C TYR 3.2 10.5 - - - +
102C CYS* 4.2 14.0 - - - -
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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