Contacts of the strand formed by residues 101 - 107 (chain C) in PDB entry 4CYM
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 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LYS 3.7 1.7 + - - +
28C VAL* 3.2 11.5 - - - -
29C LEU* 3.0 23.0 + - - +
100C VAL* 1.3 82.3 + - - +
102C ALA* 1.3 61.3 + - - +
136C ILE* 3.5 10.5 - - - +
137C PRO* 3.4 15.7 - - - -
188C LEU* 4.5 0.9 - - - -
192C ILE* 4.1 12.6 - - - -
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Residues in contact with ALA 102 (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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28C VAL* 4.2 0.7 - - - -
29C LEU* 3.4 17.7 - - + +
31C ILE* 5.2 2.0 - - + -
101C GLY* 1.3 74.9 - - - +
103C PHE* 1.3 66.7 + - - +
104C VAL* 4.1 2.2 + - + -
124C LEU* 3.7 30.5 - - + -
136C ILE* 3.9 5.2 - - + -
137C PRO 3.0 9.7 + - - +
138C ALA* 3.4 5.5 - - + -
139C VAL* 2.9 25.5 + - - -
188C LEU* 4.0 9.4 - - - +
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Residues in contact with PHE 103 (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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28C VAL* 4.3 8.3 - - + -
29C LEU 2.8 11.7 + - - +
30C VAL* 3.4 22.7 - - + -
31C ILE* 2.9 30.3 + - - +
41C ILE* 6.1 4.5 - - + -
45C TYR* 6.3 3.1 - + - -
77C LEU* 6.2 2.5 - - + -
79C LEU* 4.8 9.0 - - + -
102C ALA* 1.3 72.7 - - - +
104C VAL* 1.3 60.5 - - - +
105C VAL* 4.3 6.1 - - + -
139C VAL* 3.4 26.5 - - + +
141C LEU* 3.9 27.4 - - + -
184C ALA* 3.9 20.9 - - + -
185C ALA* 3.9 26.7 - - + -
188C LEU* 3.6 25.4 - - + -
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Residues in contact with VAL 104 (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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31C ILE* 3.4 28.9 - - + +
32C GLY* 5.0 1.6 - - - -
102C ALA* 4.9 3.6 - - + -
103C PHE* 1.3 76.8 - - - +
105C VAL* 1.3 66.5 + - - +
117C VAL* 3.9 35.2 - - + +
120C TRP* 4.4 7.9 - - + -
121C LYS* 4.9 7.6 - - + +
124C LEU* 5.0 1.1 - - + -
138C ALA* 4.7 10.8 - - + -
139C VAL 3.2 5.1 + - - +
140C LEU* 3.4 7.9 - - + +
141C LEU* 2.9 24.6 + - - +
167C PHE* 3.8 28.9 - - + -
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Residues in contact with VAL 105 (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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30C VAL* 4.1 22.4 - - + -
31C ILE 2.9 15.2 + - - +
32C GLY* 3.7 14.9 - - - -
33C GLU 4.2 0.9 + - - -
36C VAL* 3.1 32.4 - - + +
38C LYS* 4.2 4.3 - - + -
41C ILE* 3.9 21.8 - - + -
103C PHE* 4.3 2.2 - - + -
104C VAL* 1.3 84.1 - - - +
106C PHE* 1.3 66.0 + - - +
113C THR 4.9 1.0 - - - +
117C VAL* 4.8 3.0 - - - +
141C LEU* 3.6 29.2 - - + +
143C ASN* 4.0 10.1 - - + -
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Residues in contact with PHE 106 (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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36C VAL* 3.7 10.8 - - - -
105C VAL* 1.3 76.0 - - - +
107C ASP* 1.3 80.2 + - - +
108C ILE* 4.1 16.2 - - + -
113C THR* 3.4 22.7 - - - +
114C PHE* 3.5 43.5 - + + -
117C VAL* 3.9 3.8 - - + -
140C LEU* 3.8 31.0 - - + -
141C LEU 3.0 14.5 + - - +
142C ALA* 3.5 29.2 - - + -
143C ASN* 2.9 30.0 + - - +
153C GLN* 4.2 13.0 - - - -
158C VAL* 5.5 6.5 - - + -
170C TRP* 6.1 0.4 - + - -
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Residues in contact with ASP 107 (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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36C VAL* 3.4 12.2 - - + +
106C PHE* 1.3 78.5 - - - +
108C ILE* 1.3 63.9 + - - +
109C SER* 2.7 40.6 + - - -
110C ARG* 2.8 60.8 + - + +
113C THR* 3.0 12.6 + - - +
143C ASN 3.9 2.6 - - - +
144C LYS* 3.1 34.6 + - + +
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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
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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