Contacts of the strand formed by residues 119 - 128 (chain A) 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 PRO 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.8 20.2 - - + -
117A LEU 3.9 5.4 - - - +
118A GLU* 1.3 96.7 - - + +
120A GLU* 1.3 60.3 + - - +
136A MET* 3.7 21.3 - - + -
138A TRP* 3.5 23.8 - - + -
139A LYS* 3.7 13.2 - - - -
155A LYS 5.7 0.4 - - - +
156A CYS* 3.9 20.2 - - + -
159A VAL* 4.2 15.8 - - + +
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Residues in contact with GLU 120 (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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118A GLU 3.5 1.0 + - - -
119A PRO* 1.3 74.8 - - - +
121A ARG* 1.3 70.3 + - + +
137A LYS* 2.8 43.8 + - + +
138A TRP 3.7 2.0 - - - +
139A LYS* 3.5 32.9 - - + +
140A ASN 4.8 0.3 + - - -
159A VAL* 4.6 10.6 - - - +
168C LEU 4.8 1.2 - - - +
169C THR* 3.3 12.7 - - - -
170C TRP* 2.7 45.6 + - - +
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Residues in contact with ARG 121 (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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120A GLU* 1.3 87.4 - - + +
122A ILE* 1.3 76.6 + - - +
123A ILE* 4.0 11.7 - - + -
136A MET* 3.9 6.3 - - - -
137A LYS* 2.8 35.1 + - - +
159A VAL* 4.3 7.0 - - - -
162A SER* 4.2 17.1 + - - -
163A PHE* 6.4 1.6 - - - +
166A GLU* 5.7 1.0 - - - +
167A ARG* 6.1 1.6 - - - +
165C GLU 4.3 4.2 + - - -
166C GLU* 3.2 34.9 + - - +
167C ARG* 4.0 5.8 - - - +
168C LEU* 2.7 37.4 + - - +
169C THR* 4.0 14.6 - - + +
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Residues in contact with ILE 122 (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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121A ARG* 1.3 86.3 - - - +
123A ILE* 1.3 60.6 + - - +
124A GLY 3.4 22.4 - - - +
134A PHE* 3.7 38.1 - - + -
135A LEU 3.5 8.3 - - - +
136A MET* 3.6 24.5 - - + -
159A VAL* 3.7 13.7 + - + +
160A VAL* 3.7 32.3 - - + -
163A PHE* 3.4 40.2 - - + +
167A ARG* 4.5 2.9 + - - -
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Residues in contact with ILE 123 (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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121A ARG* 4.0 17.9 - - + +
122A ILE* 1.3 77.1 - - - +
124A GLY* 1.3 57.7 + - - +
135A LEU* 2.7 63.2 + - + +
136A MET 3.8 1.1 - - - -
137A LYS* 3.5 26.0 - - + +
144A ALA* 3.9 9.0 - - + -
163A PHE* 4.3 5.2 - - - -
167A ARG* 4.5 10.1 + - - +
167C ARG* 5.4 1.1 - - + +
169C THR* 4.5 5.8 - - + -
171D HIS* 5.4 2.7 - - + -
102E LEU* 3.5 32.8 - - + +
103E MET* 4.6 2.9 - - - +
104E PRO* 3.1 26.0 - - + +
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Residues in contact with GLY 124 (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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122A ILE* 3.4 12.3 - - - +
123A ILE* 1.3 81.3 - - - +
125A ALA* 1.3 63.4 + - - +
134A PHE* 3.4 1.2 - - - -
135A LEU* 2.8 28.8 + - - -
163A PHE* 3.9 9.3 - - - -
173D TYR* 3.1 20.2 - - - -
104E PRO* 4.8 0.2 - - - -
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Residues in contact with ALA 125 (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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124A GLY* 1.3 75.9 - - - +
126A THR* 1.3 71.4 + - - +
132A LEU* 4.4 9.2 - - + -
133A MET 3.2 13.5 - - - +
134A PHE* 3.8 17.5 - - + -
163A PHE* 3.9 17.8 - - + -
170B TRP* 3.3 20.7 + - + -
173D TYR* 3.0 8.1 + - - -
109E GLN 4.1 0.5 - - - +
110E THR* 4.3 2.3 - - - -
112E PHE* 4.6 12.4 - - + +
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Residues in contact with THR 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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125A ALA* 1.3 84.5 - - - +
127A ASP* 1.3 70.0 + - - +
128A SER* 5.6 2.4 - - - -
131A GLU 3.6 1.7 - - - +
132A LEU* 3.8 4.0 - - - +
133A MET* 3.1 38.2 + - - +
146A LEU* 4.9 6.1 - - - +
170B TRP* 3.8 10.7 - - - +
173D TYR* 3.3 31.1 - - + -
109E GLN* 3.4 21.8 - - + +
110E THR* 3.6 11.7 - - + -
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Residues in contact with ASP 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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126A THR* 1.3 81.6 - - - +
128A SER* 1.3 62.7 + - - +
130A GLY* 5.0 4.7 - - - +
131A GLU 3.9 6.6 + - - +
132A LEU* 4.2 14.9 + - - +
168B LEU* 6.0 0.2 - - - +
170B TRP* 3.2 38.2 - - - -
109E GLN 5.2 0.8 + - - -
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Residues in contact with SER 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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126A THR* 5.6 2.9 - - - -
127A ASP* 1.3 76.6 - - - +
129A SER* 1.3 71.1 + - - +
130A GLY 2.5 13.3 + - - +
131A GLU* 2.9 14.0 + - - +
133A MET* 3.9 21.1 - - - +
146A LEU* 6.0 1.3 - - - +
175D SER 6.3 2.9 - - - -
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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