Contacts of the strand formed by residues 98 - 103 (chain A) in PDB entry 2FK8
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 ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLY* 3.3 29.1 + - - -
75A MET 2.8 7.7 + - - -
76A THR* 3.4 21.8 + - + +
77A LEU 2.9 22.8 + - - -
97A VAL* 1.3 77.1 - - - +
99A VAL* 1.3 63.8 + - - +
123A ARG* 3.4 15.7 + - - +
124A SER* 2.7 46.8 + - - +
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Residues in contact with VAL 99 (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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77A LEU* 3.4 14.8 - - + +
88A MET* 3.8 27.8 - - + +
91A ALA* 4.3 4.0 - - + -
92A VAL* 3.6 22.2 - - + -
97A VAL* 4.1 11.7 - - + -
98A ASN* 1.3 80.1 - - - +
100A ILE* 1.3 68.8 + - - +
116A LEU* 4.2 14.1 - - + -
124A SER* 2.8 9.8 + - - +
125A ARG* 3.4 32.5 - - + -
126A GLN* 3.0 24.0 + - - +
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Residues in contact with ILE 100 (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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76A THR* 3.7 24.7 - - + -
77A LEU 2.9 8.3 + - - +
78A LEU* 3.3 21.5 - - + +
79A ASP* 2.8 26.3 + - - +
88A MET* 4.0 3.3 - - - +
99A VAL* 1.3 79.4 - - - +
101A GLY* 1.3 63.8 + - - +
102A LEU* 4.4 0.7 - - + -
126A GLN* 3.2 27.8 - - + +
128A LEU* 4.1 17.0 - - + -
135A PHE* 4.0 22.0 - - + -
137A GLU* 5.5 3.1 - - + -
138A PRO 4.9 2.5 - - - +
139A VAL* 3.9 16.6 - - + -
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Residues in contact with GLY 101 (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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79A ASP 3.5 7.0 - - - -
82A CYS* 3.8 9.4 - - - -
88A MET* 3.4 21.8 - - - -
100A ILE* 1.3 74.9 - - - +
102A LEU* 1.3 67.4 + - - +
126A GLN 2.8 11.8 + - - -
127A VAL* 3.4 1.5 - - - -
128A LEU* 2.8 26.7 + - - +
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Residues in contact with LEU 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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78A LEU* 3.9 15.7 - - + -
79A ASP 3.0 10.4 + - - +
80A ILE* 4.2 14.6 - - + -
81A GLY 2.8 25.4 + - - +
82A CYS* 2.9 9.6 + - - -
100A ILE* 4.4 0.4 - - + -
101A GLY* 1.3 83.0 - - - +
103A THR* 1.3 61.1 + - - +
128A LEU* 3.5 22.7 - - + -
130A GLN* 3.5 14.8 - - + +
131A GLY 4.1 1.1 - - - -
132A TRP* 3.7 36.3 - - + +
135A PHE* 3.9 34.1 - - + -
302A SAM 4.0 6.5 - - + -
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Residues in contact with THR 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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82A CYS* 4.0 15.0 - - - -
102A LEU* 1.3 76.8 - - - +
104A LEU* 1.3 61.8 + - - +
105A SER* 3.1 21.6 + - - +
108A GLN* 2.7 32.9 + - - -
109A HIS* 3.9 25.8 - - + +
127A VAL* 4.2 3.6 - - + -
128A LEU 3.2 7.6 + - - +
129A LEU* 3.3 9.1 - - + +
130A GLN 3.0 26.0 + - - -
302A SAM 3.1 10.8 + - - -
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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