Contacts of the strand formed by residues 124 - 126 (chain A) in PDB entry 3FTN
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.5 8.1 - - - -
28A ILE* 3.5 8.2 - - - +
29A VAL* 2.8 58.5 + - + -
31A PRO* 3.9 24.7 - - + -
61A ALA* 3.9 15.9 - - + -
63A GLY* 5.4 0.4 - - - -
83A VAL* 4.0 11.7 - - + -
112A PHE* 3.7 20.2 - + + -
117A ASP* 5.0 1.8 - - + +
118A GLY 3.7 19.5 - - - +
119A VAL* 3.7 41.7 - - + -
123A PHE* 1.3 78.1 - - - +
125A HIS* 1.3 60.9 + - - +
126A VAL* 3.7 21.8 - - + -
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Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 4.0 21.2 - - + +
21A ALA 3.6 23.3 + - - -
22A PRO* 4.5 1.1 - - + -
23A GLY 4.6 0.2 + - - -
26A ASP* 3.2 30.6 + - + -
27A ALA 3.8 3.1 - - - -
28A ILE* 4.0 11.7 - - + -
112A PHE* 3.2 17.9 - - - -
116A LYS* 2.8 50.0 + - - +
117A ASP 5.5 1.2 + - - -
124A PHE* 1.3 75.8 - - - +
126A VAL* 1.3 61.8 + - - +
127A ASN* 3.6 18.6 - - + -
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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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26A ASP* 3.4 3.3 - - - +
27A ALA* 2.9 36.1 + - + +
29A VAL* 3.8 17.0 - - + -
83A VAL* 4.1 7.4 - - + -
87A THR* 4.5 11.7 - - + -
112A PHE* 4.1 7.2 - - + -
116A LYS* 4.2 0.7 - - - +
124A PHE* 3.7 26.9 - - + -
125A HIS* 1.3 79.4 + - - +
127A ASN* 1.3 73.5 + - - +
128A ASP 3.5 0.2 + - - -
129A ALA* 4.2 3.7 + - - -
132A ASN* 4.3 11.4 - - + -
133A LEU* 4.0 26.2 - - + -
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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