Contacts of the strand formed by residues 98 - 103 (chain E) in PDB entry 2FMM
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 ARG 98 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C THR 3.6 0.3 - - - +
170C TRP* 3.5 11.3 - - - -
171C HIS* 2.9 36.6 + - - +
172C SER 5.1 2.7 - - - -
173C TYR* 3.8 36.6 - - + -
174C PRO* 4.7 8.7 - - - +
125D ALA 5.6 1.3 - - - +
166D GLU 5.4 1.0 + - - -
167D ARG* 3.5 46.1 + - - +
169D THR* 5.0 3.6 + - - -
61E GLU* 5.9 0.7 - - - -
68E ARG* 3.7 27.1 - - - +
96E GLY 3.9 7.9 - - - +
97E ARG* 1.3 77.0 - - - +
99E LEU* 1.3 64.6 + - - +
100E VAL* 3.2 29.3 + - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 4.5 19.6 - - + +
169C THR* 3.5 20.9 - - - +
170C TRP* 3.5 43.8 - - + +
125D ALA* 3.8 17.5 + - + +
126D THR* 3.8 27.1 - - - -
127D ASP* 4.1 10.5 - - + +
132D LEU* 3.8 23.3 - - + -
163D PHE* 4.6 9.4 - - - -
164D TYR* 6.0 0.2 - - - -
167D ARG* 4.5 10.4 - - - -
98E ARG* 1.3 74.4 - - - +
100E VAL* 1.3 65.3 + - - +
101E PRO* 4.7 0.5 - - - +
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Residues in contact with VAL 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU* 3.3 4.9 - - - +
169C THR* 3.0 34.3 + - - +
171C HIS* 3.8 25.8 - - + -
167D ARG* 3.5 22.4 - - + +
169D THR* 3.6 20.9 - - - +
98E ARG* 3.2 44.0 - - - +
99E LEU* 1.3 76.1 - - - +
101E PRO* 1.3 72.0 - - - +
102E LEU* 3.1 3.9 + - + -
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Residues in contact with PRO 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 3.8 29.2 - - + +
167C ARG 3.5 8.5 - - - +
168C LEU* 3.8 17.0 - - + -
164D TYR* 3.9 22.2 - - + +
167D ARG* 3.8 18.4 - - + +
168D LEU* 3.7 5.8 - - + +
169D THR* 2.9 28.8 + - - +
99E LEU 4.7 0.2 - - - +
100E VAL* 1.3 84.7 - - + +
102E LEU* 1.3 59.0 + - - +
103E MET* 3.8 20.9 - - + -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.5 23.9 - - + +
137A LYS* 3.3 40.2 - - + -
142A ASP 5.1 1.1 - - - +
167C ARG* 3.0 17.8 + - - +
169C THR* 3.4 23.1 - - + +
171C HIS* 4.1 15.3 - - + +
169D THR* 3.4 34.5 - - + +
170D TRP 4.4 0.4 - - - +
171D HIS* 4.0 30.7 - - + -
100E VAL* 3.1 3.3 + - + +
101E PRO* 1.3 72.6 - - - +
103E MET* 1.3 64.8 + - - +
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Residues in contact with MET 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.6 4.7 - - - +
124C GLY* 5.8 0.2 - - - -
125C ALA* 4.5 4.7 - - - -
163C PHE* 3.5 34.5 - - + -
164C TYR* 4.5 2.0 - - + -
167C ARG* 3.5 28.5 - - + +
168D LEU* 3.3 29.4 - - + -
169D THR 3.1 4.6 + - - +
170D TRP* 3.2 31.7 - - + -
171D HIS* 3.0 21.7 + - - -
101E PRO* 3.8 21.3 - - + -
102E LEU* 1.3 79.3 - - - +
104E PRO* 1.3 75.9 - - + +
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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