Contacts of the strand formed by residues 102 - 108 (chain L) in PDB entry 3CX5
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 GLN 102 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53L VAL 4.0 0.5 - - - +
54L VAL* 3.2 4.1 - - - -
55L PHE* 2.7 44.7 + - + +
57L SER* 3.1 23.4 + - - +
58L GLY* 4.2 1.6 - - - -
70L SER* 3.2 37.0 + - - -
96L ASN 3.5 4.3 - - - -
97L ILE* 3.5 20.5 - - + +
101L PHE* 1.3 75.8 - - - +
103L SER* 1.3 61.1 + - - +
104L TYR* 2.6 30.2 + - + +
196L PHE* 3.7 13.4 - - - -
201L PHE* 3.5 19.6 - - - -
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Residues in contact with SER 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL 3.6 3.6 - - - -
54L VAL* 4.0 18.8 - - - -
95L SER* 2.8 31.4 + - - -
96L ASN* 3.0 21.3 + - - +
101L PHE* 4.7 0.4 - - - -
102L GLN* 1.3 75.8 - - - +
104L TYR* 1.3 64.0 + - - +
105L ILE* 4.1 10.0 - - - +
388L ASN* 2.6 36.6 + - - -
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Residues in contact with TYR 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L GLY* 3.1 3.6 - - - -
53L VAL* 3.0 31.2 + - + +
55L PHE* 3.9 23.8 - + - -
70L SER 4.1 0.5 + - - -
73L TRP* 3.2 23.8 - + + +
74L LYS* 3.8 8.8 + - - -
77L PHE* 3.6 46.7 - + + -
94L SER 3.6 3.4 - - - -
95L SER* 3.4 19.5 - - - -
97L ILE* 4.2 0.7 - - + +
102L GLN* 2.6 41.4 + - + +
103L SER* 1.3 76.6 - - - +
105L ILE* 1.3 60.3 + - - +
120L LEU* 4.1 4.6 - - + +
124L PHE* 3.6 31.0 - + + -
201L PHE* 3.7 8.0 - + - -
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Residues in contact with ILE 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L SER* 3.7 28.0 - - - +
51L VAL 3.6 13.0 - - - +
52L GLY* 4.6 5.4 - - - -
53L VAL 5.4 0.2 - - - +
54L VAL* 5.6 2.7 - - + -
77L PHE* 4.1 3.0 - - - -
92L ALA 3.8 0.2 - - - +
93L LEU* 3.5 4.0 - - - -
94L SER* 2.7 50.2 + - - +
103L SER* 4.1 7.4 - - - +
104L TYR* 1.3 82.7 - - - +
106L VAL* 1.3 69.6 + - - +
107L SER* 4.2 0.4 - - - +
384L VAL* 3.7 15.3 - - + +
387L ALA* 3.6 25.1 - - + -
388L ASN* 3.4 31.2 - - - +
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Residues in contact with VAL 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ALA 4.0 0.3 - - - +
50L SER* 3.4 1.0 - - - -
51L VAL 2.7 37.4 + - - +
77L PHE* 4.4 2.7 - - + -
91L LEU* 3.6 41.5 - - + -
92L ALA 3.4 2.5 - - - +
93L LEU* 3.9 20.6 - - + -
105L ILE* 1.3 79.8 - - - +
107L SER* 1.3 62.9 + - - +
116L SER* 4.0 22.1 + - - +
119L PHE* 4.1 11.2 - - + -
120L LEU* 3.6 28.3 - - + -
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Residues in contact with SER 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L THR* 5.8 3.1 - - - -
49L ALA 3.3 5.8 - - - -
50L SER* 2.8 21.9 + - - -
90L GLY 4.0 0.2 - - - +
91L LEU* 3.3 7.4 - - - +
92L ALA* 2.8 45.0 + - - -
94L SER* 5.2 1.6 + - - -
105L ILE* 4.6 0.9 - - - +
106L VAL* 1.3 73.6 - - - +
108L SER* 1.3 65.2 + - - +
116L SER* 4.6 0.2 - - - -
384L VAL* 3.4 18.7 - - - +
323M LEU* 4.2 11.0 - - - +
327M VAL* 6.1 2.2 - - - -
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Residues in contact with SER 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L THR* 3.5 3.1 - - - -
49L ALA* 2.7 39.1 + - - +
51L VAL* 6.1 0.2 - - - +
90L GLY 4.1 2.5 - - - -
91L LEU* 3.7 17.9 - - - -
107L SER* 1.3 77.7 - - - +
109L LEU* 1.3 66.3 + - - +
112L SER* 3.3 16.2 + - - -
113L THR* 3.9 3.1 + - - -
116L SER* 3.1 22.1 + - - -
323M LEU* 3.5 16.7 - - - +
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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