Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 5FL6
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 LEU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 4.1 2.7 - - - -
91A LEU* 4.9 2.7 - - + -
121A VAL* 5.0 9.4 - - + -
122A HIS 3.3 15.5 - - - +
123A LEU* 3.9 19.7 - - + -
130A VAL* 4.4 18.4 - - + -
133A ALA* 4.1 10.0 + - + +
134A LEU* 4.0 31.6 - - + -
135A GLY 5.9 0.2 - - - +
136A ARG 4.9 0.2 + - - -
138A GLY 4.0 4.0 - - - -
139A GLY* 1.3 83.3 - - - +
141A ALA* 1.3 61.5 + - - +
142A VAL* 5.7 0.4 - - + -
199A LEU* 4.0 22.7 - - + -
205A ALA* 6.0 0.4 - - + -
207A GLY 4.0 3.9 + - - +
208A VAL* 3.5 22.4 - - + -
209A ILE* 3.1 22.3 + - - +
268A Y0R 5.9 1.6 - - - +
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Residues in contact with ALA 141 (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 MET* 4.1 16.2 - - + -
82A LEU* 4.3 11.9 - - + -
88A TYR* 3.6 29.1 - - + -
121A VAL* 3.7 0.2 - - - -
122A HIS* 2.8 43.0 + - - +
140A LEU* 1.3 74.5 - - - +
142A VAL* 1.3 63.4 + - - +
143A LEU* 5.9 0.2 - - + -
208A VAL* 4.6 0.2 - - - -
209A ILE* 3.3 12.6 - - + +
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Residues in contact with VAL 142 (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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119A HIS* 3.7 24.9 - - + -
120A VAL 3.3 7.9 - - - +
121A VAL* 4.3 15.7 - - + -
140A LEU* 5.7 0.4 - - + -
141A ALA* 1.3 79.0 - - - +
143A LEU* 1.3 68.3 + - - +
199A LEU* 5.2 4.0 - - + -
208A VAL* 3.9 19.1 - - + -
209A ILE 2.9 8.3 + - - +
210A TRP* 3.3 42.5 - - + -
211A THR* 3.0 28.8 + - - +
268A Y0R 4.2 9.0 - - - +
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Residues in contact with LEU 143 (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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48A LEU* 3.4 34.8 - - + -
50A LEU* 4.4 8.7 - - + -
53A PHE* 5.8 0.4 - - + -
80A MET* 4.1 24.9 - - + -
82A LEU* 4.5 1.6 - - + -
118A ILE 3.6 1.0 - - - +
119A HIS* 3.3 4.9 - - - -
120A VAL* 2.9 42.5 + - + +
122A HIS* 3.7 23.6 - - + -
141A ALA* 5.8 0.4 - - + -
142A VAL* 1.3 76.1 - - - +
144A ALA* 1.3 59.7 + - - +
185A LEU* 4.2 21.9 - - + +
189A PHE* 5.7 0.9 - - + -
211A THR* 3.5 17.0 - - + +
213A PHE* 4.1 14.4 - - + -
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Residues in contact with ALA 144 (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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117A GLU* 3.6 22.9 - - - +
118A ILE 3.2 4.7 - - - -
119A HIS* 3.7 10.1 - - + +
143A LEU* 1.3 75.0 - - - +
145A ALA* 1.3 59.8 + - - +
185A LEU* 5.4 0.7 - - - -
210A TRP* 4.2 10.3 - - + -
211A THR 2.8 14.7 + - - +
212A VAL* 3.3 18.1 - - + +
213A PHE* 3.0 31.8 + - - -
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Residues in contact with ALA 145 (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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117A GLU* 3.3 5.6 - - - +
118A ILE* 2.9 47.6 + - + +
144A ALA* 1.3 74.9 - - - +
146A PHE* 1.3 68.5 + - - +
147A LEU 3.8 0.2 + - - -
185A LEU* 4.4 1.8 - - + -
186A PRO* 3.5 36.8 - - + -
212A VAL* 5.6 0.4 - - - -
213A PHE* 4.0 8.7 - - + +
215A GLN 4.7 0.9 - - - +
217A VAL* 4.3 3.1 - - + -
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Residues in contact with PHE 146 (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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34A ILE* 4.9 0.2 - - + -
105A SER* 3.8 7.2 - - - -
107A HIS* 3.3 42.0 - - + -
109A VAL* 3.8 19.1 - - + -
114A PHE* 3.4 56.3 - + + -
116A ALA 3.6 1.8 - - - -
117A GLU* 3.5 22.7 - - - -
145A ALA* 1.3 74.5 - - - +
147A LEU* 1.3 62.6 + - - +
148A GLU 4.1 0.2 - - - -
193A PHE* 6.6 0.2 - + - -
212A VAL* 3.9 21.5 - - + -
213A PHE 4.5 11.4 + - - -
214A ASN 5.6 0.9 - - - -
215A GLN 5.0 0.8 + - - -
216A THR* 3.5 18.3 - - + +
217A VAL* 2.9 26.0 + - - +
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Residues in contact with LEU 147 (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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95A LEU* 4.4 12.8 - - + -
114A PHE* 4.2 0.5 - - - +
115A PRO* 3.2 23.8 - - - +
116A ALA* 2.8 46.2 + - + +
117A GLU* 4.1 3.1 - - - +
118A ILE* 4.0 14.4 - - + -
145A ALA 4.1 0.2 - - - +
146A PHE* 1.3 77.7 - - - +
148A GLU* 1.3 61.3 + - - +
157A TYR* 3.3 35.9 - - + +
217A VAL* 3.4 21.1 - - + +
219A LEU* 3.9 28.0 - - + -
224A LEU* 4.6 4.7 - - + -
227A LEU* 4.7 4.9 - - + -
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Residues in contact with GLU 148 (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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112A HIS* 4.9 4.2 + - - -
114A PHE* 3.6 28.7 - - + -
115A PRO* 4.3 11.5 - - + +
147A LEU* 1.3 77.7 - - - +
149A GLU* 1.3 64.5 + - - +
216A THR* 2.7 38.0 + - - +
217A VAL 2.8 9.1 + - - +
218A MET* 3.3 13.1 - - - +
219A LEU* 2.8 26.9 + - - +
224A LEU* 4.1 6.3 - - - -
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Residues in contact with GLU 149 (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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115A PRO* 4.8 4.1 - - + +
148A GLU* 1.3 75.1 - - - +
150A GLY* 1.3 70.6 - - - +
218A MET* 3.5 10.7 - - - +
219A LEU 3.2 4.9 - - - -
221A ALA* 3.6 36.6 + - - +
224A LEU* 3.8 14.3 - - + +
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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