Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 3FC2
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 PHE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 4.1 16.6 - - + -
39A GLU 3.5 24.0 - - - -
40A ILE* 3.4 29.6 - - + -
41A PRO* 3.7 21.3 - - + -
83A ILE* 3.7 15.3 - - + -
84A VAL 3.5 3.4 - - - +
85A PRO* 3.6 29.2 - - + -
86A LYS* 4.2 4.0 - - - -
121A GLU* 3.2 6.2 - - - +
122A ASP* 2.8 41.9 + - - +
124A ASP* 1.3 95.6 - - + +
126A VAL* 1.3 62.8 + - - +
127A PHE* 3.4 24.7 - + + -
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Residues in contact with VAL 126 (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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82A LYS 3.6 0.5 - - - +
83A ILE* 3.4 4.3 - - - +
84A VAL* 2.9 49.2 + - + +
86A LYS* 4.1 16.4 - - + -
89A LEU* 4.0 26.0 - - + -
98A MET* 4.5 8.1 - - + -
102A ILE* 4.4 23.3 - - + -
119A PHE* 5.0 4.3 - - + -
120A PHE 3.7 9.9 - - - +
121A GLU* 4.1 9.9 - - + +
125A PHE* 1.3 76.5 - - - +
127A PHE* 1.3 70.1 + - - +
128A VAL* 4.5 4.3 - - + -
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Residues in contact with PHE 127 (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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41A PRO* 4.3 7.2 - - + -
44A LEU* 3.6 31.9 - - + -
45A VAL 5.8 0.4 - - - -
82A LYS 3.5 3.8 - - - +
83A ILE* 3.7 31.9 - - + -
119A PHE* 3.1 6.9 - - - +
120A PHE* 2.8 84.8 + + + +
121A GLU* 4.0 0.7 - - - -
122A ASP* 3.9 36.8 - - + -
125A PHE* 3.4 30.1 - + + -
126A VAL* 1.3 72.1 - - - +
128A VAL* 1.3 61.9 + - - +
129A VAL* 5.5 1.3 - - + -
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Residues in contact with VAL 128 (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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80A ALA 3.6 1.4 - - - +
81A GLY* 3.4 5.7 - - - -
82A LYS* 2.9 50.7 + - + +
84A VAL* 5.7 1.3 - - + -
98A MET* 5.0 11.0 - - + -
101A GLU* 6.0 1.3 - - - +
102A ILE* 4.4 25.4 - - + -
116A PHE* 3.6 29.4 - - + -
118A GLY 3.7 3.4 - - - +
119A PHE* 4.3 1.3 - - + -
126A VAL* 4.5 7.0 - - + -
127A PHE* 1.3 77.7 - - - +
129A VAL* 1.3 64.0 + - - +
130A LEU* 3.7 21.2 + - + +
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Residues in contact with VAL 129 (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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53A TYR* 4.1 17.7 - - + +
70A ILE* 4.1 16.8 - - + -
79A PHE* 3.6 41.5 - - + -
80A ALA 3.8 2.0 - - - -
81A GLY* 4.8 0.7 - - - -
116A PHE* 3.9 0.7 - - - -
117A HIS* 2.9 32.6 + - + -
118A GLY* 2.9 28.4 + - - +
120A PHE* 4.0 26.7 - - + -
127A PHE* 5.1 1.1 - - + -
128A VAL* 1.3 73.9 - - - +
130A LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A IBI 3.5 53.2 - - + +
79A PHE* 3.5 7.4 - - - +
80A ALA* 2.7 41.8 + - + +
82A LYS* 4.5 14.1 - - + +
105A HIS* 3.8 29.4 - - + +
114A VAL* 4.1 0.9 - - + -
115A GLY 3.6 6.5 - - - +
116A PHE* 4.0 11.9 - - + -
117A HIS* 4.1 4.5 - - - -
128A VAL* 3.7 27.4 - - + +
129A VAL* 1.3 74.1 - - - +
131A GLU* 1.3 60.3 + - - +
132A LEU 3.3 0.5 + - - -
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Residues in contact with GLU 131 (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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10A IBI 3.4 23.2 - - - -
79A PHE* 4.9 2.2 - - - -
80A ALA* 4.0 0.4 - - - +
113A VAL 3.8 1.9 - - - +
114A VAL* 3.7 3.4 - - + -
115A GLY* 2.9 42.2 + - - +
117A HIS* 3.7 14.8 - - - +
130A LEU* 1.3 72.5 - - - +
132A LEU* 1.3 73.0 + - - +
133A CYS* 3.8 6.2 - - - -
185A ASN* 5.2 5.9 - - + +
191A LYS* 3.5 41.8 + - - +
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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