Contacts of the strand formed by residues 101 - 107 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS 3.7 1.9 + - - +
28A VAL* 3.2 12.2 - - - -
29A LEU* 3.0 22.5 + - - +
99A ALA* 4.5 0.2 - - - +
100A VAL* 1.3 83.8 + - - +
102A ALA* 1.3 61.3 + - - +
136A ILE* 3.5 10.9 - - - +
137A PRO* 3.4 15.5 - - - -
188A LEU* 4.5 1.1 - - - -
192A ILE* 4.1 11.9 - - - -
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Residues in contact with ALA 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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28A VAL* 4.2 0.2 - - - -
29A LEU* 3.4 18.8 - - + +
31A ILE* 5.2 2.0 - - + -
101A GLY* 1.3 75.9 - - - +
103A PHE* 1.3 65.4 + - - +
104A VAL* 4.1 2.0 + - + -
124A LEU* 3.7 29.8 - - + -
136A ILE* 3.9 5.8 - - + -
137A PRO 3.0 8.6 + - - +
138A ALA* 3.4 6.1 - - + -
139A VAL* 2.9 25.6 + - - -
188A LEU* 4.0 9.8 - - - +
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Residues in contact with PHE 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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28A VAL* 4.4 7.4 - - + -
29A LEU 2.8 12.1 + - - +
30A VAL* 3.4 23.4 - - + -
31A ILE* 2.9 28.9 + - - +
41A ILE* 6.1 4.5 - - + -
45A TYR* 6.2 3.4 - + - -
77A LEU* 6.2 2.7 - - + -
79A LEU* 4.8 9.6 - - + -
102A ALA* 1.3 73.2 - - - +
104A VAL* 1.3 60.9 + - - +
105A VAL* 4.3 6.5 - - + -
139A VAL* 3.4 25.8 - - + +
141A LEU* 3.8 28.3 - - + -
184A ALA* 3.9 20.0 - - + -
185A ALA* 3.9 27.4 - - + -
188A LEU* 3.6 25.6 - - + -
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Residues in contact with VAL 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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31A ILE* 3.4 29.6 - - + +
32A GLY* 5.0 0.7 - - - -
102A ALA* 4.9 4.0 - - + -
103A PHE* 1.3 75.0 - - - +
105A VAL* 1.3 67.1 + - - +
117A VAL* 3.9 35.7 - - + +
120A TRP* 4.3 9.0 - - + -
121A LYS* 4.9 7.0 - - + +
124A LEU* 5.0 1.6 - - + -
138A ALA* 4.7 10.3 - - + -
139A VAL 3.2 4.9 + - - +
140A LEU* 3.4 7.8 - - + +
141A LEU* 2.9 24.1 + - - +
167A PHE* 3.8 28.7 - - + -
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Residues in contact with VAL 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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30A VAL* 4.1 23.3 - - + -
31A ILE 2.9 15.0 + - - +
32A GLY* 3.6 14.9 - - - -
33A GLU 4.2 1.2 + - - -
36A VAL* 3.1 32.6 - - + +
38A LYS* 4.2 4.5 - - + -
41A ILE* 3.9 22.9 - - + -
103A PHE* 4.3 2.5 - - + -
104A VAL* 1.3 84.3 - - - +
106A PHE* 1.3 66.3 + - - +
113A THR 4.9 0.9 - - - +
117A VAL* 4.8 2.9 - - - +
141A LEU* 3.5 29.6 - - + +
143A ASN* 4.0 9.0 - - + -
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Residues in contact with PHE 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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36A VAL* 3.7 10.8 - - - -
105A VAL* 1.3 75.7 - - - +
107A ASP* 1.3 73.8 + - - +
108A ILE* 4.1 15.9 - - + -
111A SER* 6.2 0.2 - - - -
113A THR* 3.5 22.4 - - - +
114A PHE* 3.6 42.6 - + + -
117A VAL* 3.9 4.7 - - + -
140A LEU* 3.8 31.9 - - + -
141A LEU 3.0 13.2 + - - +
142A ALA* 3.5 29.2 - - + -
143A ASN* 2.8 29.6 + - - +
153A GLN* 4.2 12.6 - - - -
158A VAL* 5.5 7.2 - - + -
170A TRP* 6.1 0.4 - + - -
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Residues in contact with ASP 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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36A VAL* 3.4 11.5 - - + +
106A PHE* 1.3 76.9 - - - +
108A ILE* 1.3 62.8 + - - +
109A SER* 2.7 41.0 + - - -
110A ARG* 2.7 61.6 + - + +
113A THR* 3.0 13.1 + - - +
143A ASN 3.9 3.5 - - - +
144A LYS* 3.1 33.8 + - + +
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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